Cottonseed oil and uses

ABSTRACT

The present specification relates to the production of cotton plants and seeds and oil prepared therefrom having elevated levels of oleic and reduced levels of palmitic and linoleic acids. Furthermore, cottonseeds having low levels of cyclopropane and/or cyclopropene fatty acids and/or reduced levels of gossypol are described herein. The specification also describe FatB and CPA-FAS nucleotide and amino acid sequences derived from cotton facilitating, inter alia the direct modification of plant oil content and/or composition.

FIELD

The present specification relates to the production of cotton plants and seeds and oil prepared therefrom having elevated levels of oleic and reduced levels of palmitic and linoleic acids. Furthermore, cottonseeds having low levels of cyclopropane and/or cyclopropene fatty acids and/or reduced levels of gossypol are described herein. The specification also describe FatB and CPA-FAS nucleotide and amino acid sequences derived from cotton facilitating, inter alia the direct modification of plant oil content and/or composition.

BACKGROUND

Cotton is a dual purpose crop, producing both fiber and seed as valuable primary agricultural products. Normally, cottonseed products, including hulls (26%), linters (9%), oil (16%) and cottonseed meal (45%) represent approximately 15% of the farm value of the cotton crop (Cherry and Leffler, Seed. In “Cotton, agronomy monograph No. 24” (eds R J Kohel, C F Lewis) pp. 511-569. Crop Science Society of America, Madison, Wis., USA, 1984), while lint provides most of the remaining 85% of the value. Cottonseed oil is the most valuable product derived from cottonseed.

Cottonseed oil has a long tradition of use in food processing. Since cottonseed oil has a bland, neutral flavor that does not mask the inherent flavor of food, it is a popular and widely used oil for deep frying in the snack food and food service sector (Jones and King, Cottonseed Oil. National Cottonseed Products Associations, Inc. and the Cotton Foundation, Memphis, Tenn., USA, 1993). Cottonseed oil is also commonly used as an ingredient in marinades, dressings, pastries, margarines, and shortenings.

The nutritional and industrial value of cottonseed oil, like other vegetable oils, is affected by the composition of fatty acids in the oil, ie. the relative level of each the fatty acids in the oil, and the properties conferred by the carbon chain length and level of unsaturation of each fatty acid.

Isolated and purified cottonseed oil is composed mostly (>95%) of triacylglycerols (TAGs) that are synthesized and deposited during seed development. TAG molecules consist of three fatty acids esterified to a glycerol backbone, designated the sn-1, sn-2 and sn-3 positions. Briefly, the de novo biosynthesis of fatty acids in cotton seed, as in other oilseeds, occurs in the stroma of plastids during development and growth of the seeds, ie. before maturation. Fatty acids are then exported from the plastids in the form of acyl-CoA thioesters to the cytoplasmic endomembrane systems (endoplasmic reticulum, ER) where modification of fatty acids occurs after transfer of the acyl groups from the CoA thioesters to phospholipids by acyltransferases. This is followed by TAG assembly and storage in the oleosomes.

The biotin-containing enzyme acetyl-CoA carboxylase (ACCase) catalyses the first committed step in the pathway by activating acetyl-CoA to the three carbon intermediate, malonyl-CoA, by addition of a carboxyl group. The malonyl group is then transferred from CoA to an acyl-carrier protein (ACP), which serves as the carrier for the growing fatty acid chain. Malonyl-ACP is reacted with a second acetyl-CoA condensing enzyme, ketoacyl-ACP synthase III (KASIII), resulting in a four carbon chain. The repeated process of adding two-carbon units on the elongated fatty acid chain is catalyzed by KASI leading to the formation of palmitoyl-ACP. KASII catalyzes the elongation of palmitoyl-ACP to stearoyl-ACP. A soluble stearoyl-ACP Δ9-desaturase introduces the first double bond into stearoyl-ACP to convert it to oleoyl-ACP in the plastid. The extended, saturated fatty acyl chain and the monounsaturated oleate are cleaved off the ACP by a specific thioesterase enzyme, FatB or FatA, respectively, enabling them to exit the plastid and enter the cytoplasm. Saturated fatty acids released into the cytoplasm are not further modified. However, oleic acid can be further modified on the endoplasmic reticulum (ER) membranes by the action of membrane-bound desaturases. Phosphatidylcholine (PC)-bound acyl chains serve as a substrate for ER localized, lipid modifying enzymes, such as fatty acid desaturase 2 (FAD2) which introduces a double bond into oleic acid on the sn-2 position of PC to produce linoleic acid. All the modified and unmodified fatty acyl groups then form a pool while attached to CoA. In cotton, but not in other temperate zone oilseeds, oleic acid may be used as substrate for cyclopropanation catalysed by cyclopropane fatty acid synthase to produce dihydrosterculic acid. This fatty acid is subsequently desaturated to produce sterculic acid and then α-oxidased to produce malvalic acids. Finally fatty acyl groups are incorporated into storage lipids via the Kennedy pathway by the sequential esterification of glycerol-3-phosphate by the action of a series of TAG assembly enzymes.

The enzyme acyl-ACP thioesterase (FatB) (EC 3.1.2.14) catalyses the hydrolysis of the thioester bond between the acyl moiety and ACP in acyl-ACP and the release of free fatty acid in the plastid. The free fatty acid is then re-esterified to CoA in the plastid envelope as it is transported out of the plastid. FatB belongs to a class of nuclear encoded, soluble, fatty acid thioesterase (FAT) enzymes which are first translated as a precursor proteins. The substrate specificity of the FAT enzymes in the plastid is therefore involved in determining the spectrum of chain length and degree of saturation of the fatty acids exported from the plastid. FAT enzymes can be classified into two classes based on their substrate specificity and nucleotide sequences, FatA and FatB (Jones et al., Plant Cell 7: 359-371, 1995). FatA prefers oleoyl-ACP as substrate, while FatB shows higher activity towards saturated acyl-ACPs of different chain lengths. Genes encoding FatB enzyme were first isolated from plant species accumulating medium chain-length saturated fatty acids such as lauric acid (C12:0) from California bay tree (Umbellularia californica). Overexpression of the U. californica FatB1 gene in transgenic canola led to production of high-laurate oil with laurate comprising 50% of the total fatty acids in the oil (Voelker et al., Plant Journal 9: 229-241, 1996). Subsequent studies demonstrated that several FatB orthologues are present in tissues of plants, including in seeds, with substrate specificity ranging from C8:0-ACP to C18:0-ACP.

Cottonseed oil produced by conventional (wild-type) upland cotton (G. hirsutum) typically contains approximately 26% palmitic acid (range 22-28%), 2% stearic acid, 15% oleic acid (range 13-18%) and 58% linoleic acid (range 52-60%) (Cherry, J. Am. Oil Chem. Soc. 60: 360-367, 1983; O'Brien, Cottonseed Oil. In: F. D. Gunstone (Ed.) Vegetable Oils in Food Technology: Composition, Properties and Uses. Blackwell Publishing, Oxford, pp. 203-230, 2002). In addition to these fatty acids which are also present in most other temperate zone oilseed crops, unhydrogenated cottonseed oil also contains low levels (0.5-1%) of cyclopropane or cyclopropene fatty acids, mainly malvalic, sterculic and dihydrosterculic acids (Shenstone and Vickery, Nature 190: 68-169, 1961; Cherry, 1983 (supra)). Cyclopropane (CPA) and cyclopropene (CPE) fatty acids are found in the seed oils of plants in the order of Malvales and some gymnosperms, including in cotton. Two Sapindaceae species, Lychee (Litchi chinensis) and Longan (Euphoria longan) contain up to 40% CPA fatty acids in their seedoils, mostly as dihydrosterculic acid (DHS). The seed oil of Sterculia foetida contains up to 78% CPE fatty acids, mainly sterculic (STC) and malvalic acids (MVL). Unhydrogenated cottonseed oil contains relatively small amounts (0.5-1.0%) of CPE and CPA fatty acids, mostly in embryo axes. Cotton roots and hypocotyls are also found to accumulate low levels of STC and MVL. CPA and CPE are not found at detectable levels in major oilseed crops other than cotton, including in palm oil, soybean, corn, canola, mustard, sunflower, safflower, peanut, linseed, other Brassicas etc.

The First committed step to produce these uncommon fatty acids is catalysed by a cyclopropane fatty acid synthase (CPA-FAS) which adds a methylene group across the double bond of oleic acid to produce DHS (FIG. 2). In cotton, most of the DHS is desaturated by the enzyme CPA desaturase to produce STC, most of which is further modified by α-oxidation to form MVL (FIG. 2). MVL is the predominant cyclopropenoid fatty acid in wild-type cottonseed oil.

The relatively high level of saturated fatty acids, mainly palmitic acid, in cottonseed oil compared to oils from most other temperate zone oilseed crops contributes to the oxidative stability of cottonseed oil by offsetting the greater instability of the other, unsaturated fatty acid components. It also imparts the high melting point required for making such products as margarine and shortening. On the other hand, higher levels of palmitic acid are nutritionally less desirable because of its property of raising LDL-cholesterol in humans, associated with increased risk of cardiovascular heart disease (CHD) (Lindsey et al., Exp. Biol. Med. 195: 261-269, 1990). Except for palm oil, cottonseed contains the highest palmitic acid level (26%) among the major commodity vegetable oils. Palmitic acid and other shorter chain saturated fatty acids are widely reported to raise total plasma cholesterol and low density lipoprotein cholesterol levels (Kris-Etherton et al., Nutrition-today (USA). 28: 30-38, 1993). Cottonseed oil also contains a high level of linoleic acid which is oxidatively unstable and therefore limits the shelf life of the oil and makes it unsuitable for some food applications.

Conventional cottonseed oil is therefore often processed by partial hydrogenation during which the polyunsaturated linoleic acid is transformed into more stable monounsaturated (oleic) and saturated (stearic) fatty acids. Partial hydrogenation results in a number of structural changes to a fraction of the fatty acids, including the shifting of a double bond. This may lead to the production of trans fatty acids (TFA) which are isomers of the naturally occurring unsaturated fatty acids. In most naturally occurring unsaturated fatty acids such as oleic acid, the two hydrogen atoms joined to the double-bonded carbon atoms are on the same side of the double bonds of the carbon chain, and this is termed a cis double bond. However, partial hydrogenation re-configures some of the double bonds so that the two hydrogen atoms are on opposite sides of the carbon-carbon double bond, as it is the lower energy form, and this is termed the trans configuration. Thus partial hydrogenation produces trans fatty acids, such as elaidic acid from oleic acid. Oleic and elaidic acids contain the same number of atoms (C18:1), with a double bond in the same location, but it is the conformation of the double bond that sets them apart. TAG containing elaidic acid, with the trans double bond configuration, has a much higher melting point than oleic acid. In recent years TFA have been increasingly recognized to have significant LDL-cholesterol raising and HDL-cholesterol lowering properties and therefore increases the risk of cardiovascular disease based on evidence derived from epidemiologic and clinical studies (Oomen et al., Lancet 357: 746-751, 2001; Mozaffarian et al., N. Engl. J. Med. 354: 1601-1613, 2006). Partial hydrogenation also converts cyclopropanoic or cyclopropenoic fatty acids to branched chain fatty acids by opening up the cyclopropane ring, producing a branched fatty acid with a additional methyl group attached to C9 or C10 of the fatty acid carbon chain.

Compared with polyunsaturated fatty acids, oleic acid is more stable towards oxidation both at ambient storage temperatures and at the high temperatures used in cooking and frying of food. Studies with a number of vegetable oils such as safflower and soybean oils indicate that high-oleic vegetable oils are slower to develop rancidity during storage, or to oxidatively decompose during frying or other use, compared to oils that contain high amounts of polyunsaturated fatty acids (Fuller et al., J. Food Sci. 31: 477-480, 1966; Mounts et al., J. Am. Oil Chem. Soc. 65: 624-628, 1998).

As mentioned above, cottonseed oil is also characterized by the presence of small amounts of malvalic, sterculic and dihydrosterculic acids, a group of cyclic propane fatty acids derived from oleic acid. It is known that malvalic and sterculic acids are potent inhibitors of animal Δ9-stearoyl-CoA desaturase. Although the CPA and CPE fatty acids are not stable and are mostly eliminated during oil processing, particularly by hydrogenation, the residual oil in the meal and the whole cottonseed used in the feed industry could exert negative effects on animal health. Feeding farmed animals with excess amounts of cottonseed is thought to possibly cause a number of health problems for animals and may affect the quality of animal products, such as the hardening of fats in egg yolk and milk (Johnson et al., Nature 214: 1244-1245, 1967; Roehm et al., Lipids 5: 80-84, 1970). Methods have been developed to inactivate cyclopropenoid fatty acids through specialised partial hydrogenation processes. Merker and Mattil, 1965 reported a hydrogenation process in which malvalic and sterculic acids were selectively reduced to their dihydro or tetrahydro derivatives, by means of a nickel catalyst, without significant reduction of the linoleic acid or trans acid formation. Hutchins et al., Journal of American Oil Chemists Society 45: 397-399, 1968 showed selective hydrogenation of the cyclopropenoid groups in cottonseed oil by means of a packed-bed reactor and nickel catalysts under milder conditions. However, these hydrogenation processes add additional costs for processing of the oil and are not desirable.

In the 1970's, the cotton breeding program of the Acala SJ series in California (Cherry, 1983 (supra)) reduced palmitic acid from 23.3 to 22.7%, increased oleic acid from 16.6% to 17.3% and reduced total cyclic fatty acids from 0.9% to 0.8% in cottonseed oil. However, compared to achievements in other oilseed crops, these changes were only minor, reflecting the narrow genetic base of elite cotton varieties as a result of persistent selection on traits other than oil quality.

Four different cDNAs encoding FAD2 were isolated from cotton (Liu et al., Australian Journal of Plant Physiology 26: 101-106, 1999a; Liu et al., Plant Physiol. 120: 339, 1999b; Pirtle et al., Biochim. Biophys. Acta 1522: 122-129, 2001, all herein incorporated by reference), among which ghFAD2-1 was determined to play a major role in the production of linoleic acid in cottonseed oil. Analysis of gene expression suggested that the ghFAD2-1 gene was specifically expressed in developing seeds, with maximal expression during the middle maturity stage of seed development (Liu et al., 1999a (supra)).

U.S. Pat. No. 6,974,898 (herein incorporated by reference) describes the generation of cottonseed oil containing up to 77% oleic acid by downregulation of microsomal Δ12 desaturase (FAD2) by RNAi methods.

Chapman et al., J. Am. Oil Chem. Soc. 78: 941-947, 2001, herein incorporated by reference, transformed cotton plants with a construct encoding a non-functional, mutant allele of fad2, obtained from rapeseed, and expressed from a seed-specific phaseolin promoter in sense orientation. About half of the 43 transgenic lines that were generated showed slightly increased oleic acid content in seedoil, ranging from 24-30%. In subsequent generations, seeds with higher levels of oleic acid up to 40% were identified.

Arabidopsis fatB mutants which had seedoil with reduced palmitic acid levels showed reduced vegetative growth under normal temperatures (Bonaventure et al., Plant Cell 15: 1020-1033, 2003). However, in previous studies with antisense constructs to down-regulate AtFatB in Arabidopsis, using the CaMV35S promoter to express the antisense RNA, a substantial reduction of palmitic acid levels was observed only in flowers and seeds, not in leaves and roots, and there was no obvious visual phenotype (Dormann et al., Plant Physiol. 123: 637-644, 2000, herein incorporated by reference).

In cotton, as in many temperate plants, FatB enzymes appear to be encoded by a multigene family. Yoder et al., Biochimica et Biophysica Acta 1446: 403-413, 1999, herein incorporated by reference, isolated a genomic DNA sequence which was thought to encode a acyl-ACP thioesterase in cotton.

Wilson et al., J. Am. Oil Chem. Soc. 78: 335-340, 2001 and Buhr et al., Plant J. 30: 155-163, 2002, both herein incorporated by reference, used antisense and ribozyme approaches, respectively, to reduce palmitic acid in soybean seeds.

A CPA-FAS gene was recently isolated from Sterculia foetida using an EST based approach (Bao et al., Proc. Natl. Acad. Sci. U.S.A. 99: 7172-7177, 2002). Two EST sequences from G. hirsutum were identified as being differentially expressed by infection of cotton roots/hypocotyls following inoculation of Fusarium (Dowd et al., Molecular Plant-Microbe Interactions. 17: 654-667, 2004, herein incorporated by reference).

There is therefore a need for improved cottonseed oil.

SUMMARY

Throughout this specification, unless the context requires otherwise, the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated element or integer or group of elements or integers but not the exclusion of any other element or integer or group of elements or integers. Each embodiment is to be applied mutatis mutandis to every other embodiment unless expressly stated otherwise.

As used herein the singular forms “a”, “an” and “the” include plural aspects unless the context clearly dictates otherwise. Thus, for example, reference to “a mutation” includes a single mutation, as well as two or more mutations; reference to “an agent” includes one agent, as well as two or more agents; and so forth.

Bibliographic details of the publications referred to by author in this specification are collected at the end of the description.

The reference in this specification to any prior publication (or information derived from it), or to any matter which is known, is not, and should not be taken as an acknowledgment or admission or any form of suggestion that that prior publication (or information derived from it) or known matter forms part of the common general knowledge in the field of endeavour to which this specification relates.

The term “derived from” indicates that the specified integer is obtained from a specific source although not necessarily directly from that source.

The designation of exemplary amino acid sequences is set out in Table 5.

Nucleotide and amino acid sequences are referred to by a sequence identifier number (SEQ ID NO:). The SEQ ID NOs: correspond numerically to the sequence identifiers <400>1 (SEQ ID NO:1), <400>2 (SEQ ID NO:2), etc. A summary of sequence identifiers is provided in Table 4. A sequence listing is provided after the claims.

Genes and other genetic material (eg mRNA, nucleic acid constructs etc) are represented herein in italics while their proteinaceous expression products are represented in non-italicised form.

In one embodiment, the present specification describes a method of producing modified cottonseed oil, comprising the steps of (i) obtaining cottonseed, (ii) extracting the oil from the cottonseed, and (iii) recovering the cottonseed oil, wherein the cottonseed oil has a modified fatty acid composition such that 72% to 88% of the total fatty acid content in the cottonseed oil is oleic acid, 4% to 16% is palmitic acid and 4% to 15% is linoleic acid. In some embodiments, 74% to 86% of the total fatty acid content of the cottonseed oil is oleic acid. In other embodiments, 4% to 10% is palmitic acid. In other embodiments, 4% to 12% is linoleic acid. In relation to trans fatty acids, in some embodiments, the cottonseed oil has less than 0.5%, preferably less than 0.1%, of the total fatty acid content is a trans fatty acid. In some embodiments, the trans fatty acid is elaidic acid. In some embodiments. 0.1% to 0.5% of the total fatty acid content in the cottonseed oil is cyclopropane fatty acid (CPA) or cyclopropene fatty acid (CPE). In particular embodiments, the cyclopropane or cyclopropene fatty acid is malvalic acid, sterculic acid, dihydrosterculic acid or any combination of two of these or all three of these. In other embodiments, less than 0.5%, preferably less than 0.1%, of the total fatty acid content is a branched fatty acid at C9 or C10. In preferred embodiments, the total fatty acid content of the seedoil has the composition of 74% to 86% oleic acid, 4% to 10% palmitic acid, 4% to 12% linoleic acid, and optionally 0.1% to 0.5% in total of cyclopropane fatty acid (CPA) and cyclopropene fatty acid (CPE), and optionally less than 1.0%, preferably less than 0.5%, more preferably less than 0.1%, of the total fatty acid content is a trans fatty acid.

In some embodiments, the production method further comprises harvesting lint comprising the cottonseed from a cotton plant and/or ginning the cottonseed from lint comprising the cottonseed. Alternatively or in addition, step (ii) comprises crushing the cottonseed and/or solvent extraction of the crushed cottonseed. In a further embodiment, step (iii) comprises purifying the cottonseed oil. Purifying the seedoil may comprise degumming the oil, decolorizing the oil, deodorizing the oil, altering the pH of the oil, hydrolyzing the oil, or any combination thereof.

Advantageously, in some embodiments, the method does not comprise a step of hydrogenation or partial hydrogenation of the cottonseed oil. Without limitation to any particular mode of action, the low level of linoleic acid and relatively high level of oleic acid obviates the need to stabilise the fatty acids, and thus avoids the de novo production of trans fatty acids induced by some forms of hydrogenation.

Accordingly, in another aspect, the specification provides cottonseed oil having a modified fatty acid composition, wherein 72% to 88% of the total fatty acid content in the cottonseed oil is oleic acid, 4% to 16% is palmitic acid and 4% to 15% is linoleic acid. In some embodiments, 74% to 86% of the total fatty acid content of the cottonseed oil is oleic acid. In other embodiments, 4% to 10% is palmitic acid. In other embodiments, 4% to 12% is linoleic acid. In some embodiments, 0.1% to 0.5% of the total fatty acid content in the cottonseed oil is cyclopropane fatty acid (CPA) or cyclopropene fatty acid (CPE). In particular embodiments, the cyclopropane or cyclopropene fatty acid is malvalic acid, sterculic acid, dihydrosterculic acid or any combination of two of these or all three of these. In preferred embodiments, the total fatty acid content of the seedoil has the composition of 74% to 86% oleic acid, 4% to 10% palmitic acid, 4% to 12% linoleic acid, and optionally 0.1% to 0.5% in total of cyclopropane fatty acid (CPA) and cyclopropene fatty acid (CPE), and optionally less than 1.0%, preferably less than 0.5%, more preferably less than 0.1%, of the total fatty acid content is a trans fatty acid.

In another aspect, the specent specification provides cottonseed having a modified fatty acid composition in its oil, wherein 72% to 88% of the total fatty acid content in the oil of the cotton seed is oleic acid, 4% to 16% is palmitic acid and 4% to 15% is linoleic acid. In other embodiments, 74% to 86% of the total fatty acid content in the oil of the cotton seed is oleic acid. In other embodiments, 4% to 10% is palmitic acid. In other embodiments, 4% to 12% is linoleic acid. In still further embodiments, 0.1% to 0.5% of the total fatty acid content in the oil is a cyclopropane fatty acid (CPA). In still yet further embodiments, the cottonseed has a reduced level of gossypol, wherein the level of gossypol in the cottonseed is reduced by at least 10% relative to the level of gossypol in cottonseed of cotton variety Coker. In preferred embodiments, the total fatty acid content of the seedoil has the composition of 74% to 86% oleic acid, 4% to 10% palmitic acid, 4% to 12% linoleic acid, and optionally 0.1% to 0.5% in total of cyclopropane fatty acid (CPA) and cyclopropene fatty acid (CPE), and optionally less than 1.0%, preferably less than 0.5%, more preferably less than 0.1%, of the total fatty acid content is a trans fatty acid.

In some embodiments the specification provides cottonseed or cottonseed oil recovered therefrom wherein the cottonseed is transgenic for a genetic construct which encodes an RNA molecule which inhibits expression of two or more genes which are selected from the group consisting of FAD2, FatB-2 and CPA-FAS-2. In some embodiments the genes are ghFAD2-1, ghFatB-2 and ghCPA-FAS-2. In an illustrative embodiment, the genetic construct comprises the MonoCott construct described schematically in FIG. 12. In another embodiment, the cottonseed is transgenic for a genetic construct which encodes an RNA molecule which inhibits expression of two genes which are ghFAD2-1 and ghFatB-2. In another illustrative embodiment, the cottonseed is of the species Gossypium hirsutum or Gossypium barbadense.

In another aspect the specification described a method of producing the herein described cottonseed comprising harvesting lint from a cotton plant and ginning the lint, thereby producing the cottonseed. In another embodiment, the method comprises sowing the herein described cottonseed and allowing the seed to grow into the cotton plant.

The present invention provides a cotton plant which is capable of producing the herein described cottonseed and cotton lint obtained from said cotton plant.

Pursuant to the present invention, the specification provides a method of identifying cottonseed which has a modified fatty acid composition in its oil, comprising (i) obtaining transgenic cottonseed, (ii) determining the fatty acid composition of the oil of the cottonseed, and (iii) if 72% to 88% of the total fatty acid content in the oil of the cotton seed is oleic acid, 4% to 16% is palmitic acid and 4% to 15% is linoleic acid, selecting the cottonseed. In some embodiments, the method further comprises transformation of a cotton cell with a genetic construct and regeneration of a transgenic cotton plant prior to step (i). In some embodiments, the cottonseed of step (i) is transgenic for a genetic construct which encodes an RNA molecule which inhibits expression of two or three genes which are ghFAD2-1 and ghFatB-2 or ghFAD2-1 and ghFatB-2 and ghCPA-FAS-2. In some embodiments, the method comprises the step of selecting a cottonseed having a modified fatty acid composition in its oil, wherein 72% to 88% of the total fatty acid content in the oil of the cotton seed is oleic acid, 4% to 16% is palmitic acid and 4%© to 15% is linoleic acid. In some embodiments, the method further comprises the steps of producing a cotton plant from the seed and crossing said cotton plant with a second cotton plant, preferably of a different genetic background.

Accordingly, the specification contemplates the use of the herein described cottonseed to produce isolated oil or cottonseed meal and the use of the cotton seed as animal feed or in the production of a food product or as fuel. It is contemplated that the oil is used to increase the oleic acid content or to reduce the palmitic acid content of the food product. Alternatively or in addition the oil is used to reduce the level of, or the intake of, saturated fatty acids or trans fatty acids in the food product or by the animal. It would be understood that this is relative to the use of an equal amount of an unmodified cottonseed, oil or cottonseed meal.

In a particular embodiment, the specification provide a food product comprising a food ingredient which is the cottonseed oil as described herein.

In another aspect the invention provides a method of preparing a fried food product, comprising frying a food product in the cottonseed oil as described according herein.

The subject product may be used therapeutically and the present invention contemplates a method for treating or preventing a disease in a subject, comprising administering orally to the subject, the cottonseed oil, the cottonseed or the food product as described herein. In some embodiments, the disease is obesity, heart disease, high serum TAG content, high serum cholesterol, high serum LDL, low serum HDL, hypertension, cancer, diabetes, or any combination thereof. Any subject who could benefit from the present methods or compositions is encompassed. The term “subject” includes, without limitation, humans and non-human primates, livestock animals, companion animals, laboratory test animals, captive wild animals, reptiles and amphibians, fish, birds and any other organism. A subject, regardless of whether it is a human or non-human organism may be referred to as a patient, individual, subject, animal, host or recipient. In a particular embodiment the subject is a human.

In a particular aspect, the specification describes a nucleic acid molecule encoding a chimeric gene silencing nucleic acid which reduces gene expression of two or more genes selected from cotton FatB, cotton FAD2 and cotton CPA-FAS in a cotton plant. In some embodiments, the gene-silencing nucleic acid reduces gene expression of cotton FAD2-1 and cotton FatB-2, or cotton FAD2-1 and cotton FatB-2 and CPA-FAS-2. In some embodiments, the nucleic acid molecule comprises: (i) a contiguous sequence of nucleotides set forth in SEQ ID NO: 17 or a complementary form thereof, or a sequence having 90% identity thereto or a sequence that hybridizes to a complement thereof under high stringency hybridization conditions, or (ii) a variant of the nucleic acid molecule of (i) lacking sequences encoding to CPA-FAS-2 polypeptide or their complementary forms. In an illustrative embodiment the gene-silencing nucleic acid molecule is a hairpin RNA. In some embodiments the nucleic acid molecule is provided within a genetic construct.

In some embodiments, the gene construct comprises the nucleic acid and further comprises the structure set out in FIG. 12 or the sequences of Fragments A, E, F, G, and H set out in FIG. 13, or a functional variant thereof. In other embodiments, the nucleic acid molecule is provided in a host cell. In other embodiments, a plant or tissue or cell therefrom is provided comprising a subject nucleic acid. In some embodiments, the nucleic acid molecules are used to reduce expression of cotton FAD2-1, cotton FatB-2 and/or cotton CPA-FAS-2 genes in a cotton plant. The specification provides therefore a modified cotton plant or seed therefrom comprising a reduced level of one or more endogenous genes selected from cotton FAD2, cotton FatB and CPA-FAS, preferably two or more of said genes or all three genes wherein the cottonseed oil therein or therefrom exhibits elevated levels of oleic acid or reduced levels of palmitic acid and linoleic acid.

In a further embodiment, the cottonseed oil exhibits reduced levels of cyclopropene and/or cyclopropane fatty acids, or gossypol.

In another aspect, the specification provides an isolated nucleic acid molecule comprising a nucleotide sequence encoding a polypeptide having cotton FatB activity or a functional fragment or variant thereof, or a complementary form thereof, said nucleotide sequence selected from the group consisting of: (i) a nucleotide sequence having at least 90% identity to the nucleotide sequence of the protein encoding region of the nucleotide sequence set forth in SEQ ID NO: 5 or 7; (ii) a nucleotide sequence encoding a polypeptide having at least 80% sequence identity to the amino acid sequence set forth in SEQ ID NO: 6 or 7; (iii) a nucleotide sequence that hybridizes under at least moderate stringency hybridization conditions to at least 30 contiguous nucleotides derived from SEQ ID NO: 5 or 7; (iv) a nucleotide sequence that is complementary to (i), (ii) or (iii); and (v) a nucleotide sequence comprising nucleotides 548-843 of SEQ ID NO: 5. In some embodiment, the nucleic acid, particularly RNA, or a functional variant or fragment thereof is provided as a sense, antisense, ribozyme, co-suppression, or double-stranded RNA or other gene-silencing agent. Thus the specification provides an antisense or co-suppression molecule which comprises a fragment of any one of (i)-(v) above which is expressed and reduces expression of a cotton FatB gene.

In another embodiment, an isolated probe or primer is provided comprising at least 15 contiguous nucleotides derived from SEQ ID NO: 5 or SEQ ID NO: 7 or a complementary form thereof.

In another aspect, the specification provides an isolated nucleic acid molecule comprising a nucleotide sequence encoding a polypeptide having cotton CPA-FAS activity or a functional fragment or variant thereof, or a complementary form thereof, said nucleotide sequence selected from the group consisting of: (i) a nucleotide sequence having at least 90% identity to the nucleotide sequence of the protein encoding region of the nucleotide sequence set forth in SEQ ID NO: 10, 12 or 14; (ii) a nucleotide sequence encoding a polypeptide having at least 80% sequence identity to the amino acid sequence set forth in SEQ ID NO: 11, 13 or 15; (iii) a nucleotide sequence that hybridizes under at least moderate stringency hybridization conditions to at least 30 contiguous nucleotides derived from SEQ ID NO: 10, 12 or 14; (iv) a nucleotide sequence that is complementary to (i), (ii) or (iii); and (v) a nucleotide sequence comprising 442 nucleotides of CPA-FAS-2 encoding sequences set forth in Fragment 13 of FIG. 13. In some embodiment, the nucleic acid, particularly RNA, or a functional variant or fragment thereof is provided as a sense, antisense, ribozyme, co-suppression, or double-stranded RNA or other gene-silencing agent. Thus the specification provides an antisense or co-suppression molecule which comprises a fragment of any one of (i)-(v) above which is expressed and reduces expression of a cotton CPA-FAS-2 gene.

In another embodiment, an isolated probe or primer is provided comprising at least 15 contiguous nucleotides derived from SEQ ID NO: 10, SEQ ID NO: 12 or SEQ ID NO: 14 or a complementary form thereof.

The above summary is not and should not be seen in any way as an exhaustive recitation of all embodiments of the present invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a simplified schematic diagram of fatty acid biosynthesis in developing cottonseed showing important enzymatic steps: 1. keto-acyl synthase II (KASIII), 2. keto-acyl synthase I (KASI), 3. keto-acyl synthase II (KASII), 4. Δ9-stearoyl-ACP desaturase (SAD), 5, oleoyl-ACP thioesterase, 6. acyl-ACP thioesterase, 7. Δ12-oleoyl-lipid desaturase (FAD2), 8. cyclopropane fatty acid synthase (CPA-FAS), 9. cyclopropane fatty acid desaturase (CPA-FAD), 10. α-oxidase. DHS: dihydrosterculic acid; STC, sterculic acid; MVL, malvalic acid.

FIG. 2 is a schematic representation of biosynthesis of cyclopropane (CPA) and cyclopropene (CPE) fatty acids in developing cottonseed. Oleic acid is the fatty acid substrate for cyclopropane fatty acid synthase (CPA-FAS). S-adenosyl-L-methionine is the methylene donor and the cyclopropanation of oleic acid is catalysed by CPA-FAS, producing dihydrosterculic acid (DHS). DHS can be further modified by desaturation by the enzyme CPA desaturase to produce sterculic acid (STC). Subsequently, malvalic acid (MVL) is produced by α-oxidation of STC catalysed by an oxidase.

FIG. 3 is a representation of the nucleotide sequence of cDNA corresponding to the ghFAD2-1 gene, and the predicted amino acid sequence of the encoded precursor ghFAD2-1 polypeptide. The protein encoding region is from nucleotides 73 to 1227 (TAA stop codon).

FIG. 4 is a representation of the nucleotide sequence of cotton acyl-ACP thioesterase (ghFatB-2) cDNA and the predicted amino acid sequence of the precursor polypeptide ghFatB-2 encoded by cDNA. The protein encoding region is from nucleotides 210 to 1472 (TAG stop codon).

FIG. 5 is a representation of the nucleotide sequence of cotton acyl-ACP thioesterase (ghFatB-3) cDNA and the predicted amino acid sequence of the precursor polypeptide ghFatB-3 encoded by cDNA. The protein encoding region is from nucleotides 97 to (TAG stop codon).

FIG. 6 is a representation of the DNA sequence of the EST sequence CD486555 referred to in Example 4.

FIG. 7 is a representation of the DNA sequence of ghCPA-FAS-1 and the putative polypeptides it encodes

FIG. 8 is a representation of the DNA sequence of ghCPA-FAS-2 and the putative polypeptides it encodes

FIG. 9 is a representation of the DNA sequence of ghCPA-FAS-3 and the putative polypeptides it encodes

FIG. 10 is a representation of the Southern blot analysis of CPA-FAS genes in cotton. Total genomic DNAs from various diploid or tetraploid Gossypium species were digested with HindIII. Lane 1, G. barbadense (A+D genomes); lane 2, G. hirsutum cv. Deltapine-16 (A+D genomes); lane 3, G. hirsutum cv Sicala-V4 (A+D genomes); lane 4, G. herbaceum (A genome); lane 5, G. raimondii (ID geneome).

FIG. 11 is a representation of the RNA Northern blot analysis of expression of ghCPA-FAS-1 (A) ghCPA-FAS-2 (B) genes in cotton. RNA samples blotted onto the membrane were derived from: lane 1, cotyledon; 2, hypocotyl; 3, leaf; 4, root; 5-9, developing cotton embryos at 25, 30, 35, 40, 45 days after anthesis, respectively; 10, embryo axis.

FIG. 12 is a schematic diagram of the chimeric transgene used to generate triple-gene silencing in cotton (MonoCott construct). DNA sequences of the fragments labelled on the top of the construct are detailed in FIG. 11. (Abbreviations: LB: T-DNA left border; LecP: soybean lectin promoter; ghFAD2-1: cotton microsomal oleoyl Δ12 desaturase cDNA; ghCPA-FAS-2: cotton cyclopropane fatty acid synthase; ghFatB-1: cotton palmitoyl-ACP thioesterase; lec-T: soybean lectin terminator; RB2: T-DNA right border 2; S1: subterranean clover stunt virus segment 1 promoter; S3: subterranean clover stunt virus segment 3 terminator; NPTII: neomycin phosphotransferase gene. The sizes of the full length cDNA and the selected fragments of each target gene in making the RNAi construct were also indicated).

FIG. 13 is a representation of the DNA sequences used to make the RNAi construct illustrated in FIG. 12. Fragment A is the seed-specific Lec1 promoter; Fragment B is the chimeric fragment of the three target genes, including ghFAD2-1 (underlined), ghCPA-FAS-2 (italic font), and ghFatB-2 (bold font); Fragment C is the ghFAD2-1 intron used to separate the inverted repeats. Fragment D is the inverted repeat of fragment B; Fragment E is the lectin gene transcription terminator/polyadenylation sequence; Fragment F is the s1 promoter controlling the expression of the selectable marker gene (F+G+H); Fragment G is the NPTII protein coding region conferring kanamycin resistance and used as the selectable marker; Fragment H, the s3 transcription terminator/polyadenylation sequence.

FIG. 14 is a graphical representation of the accumulation of palmitic and oleic acids in individual seeds of three generations of DCS9-34: T₂ seeds borne on the primary transgenic line (A); T₃ seeds borne on the selected T₂ plant (B) and T₄ seeds borne on a selected T₃ plant (C).

FIG. 15 is a graphical representation of the accumulation of total cyclic fatty acids in the excised embryo axes of individual cotton seeds. DCS9-34 is the MonoCott line with HO, LP and low-cyclic fatty acids traits; LY-2 is the line with HO and LP traits; and increased cyclic fatty acids; Coker315 is the conventional or control cotton.

DETAILED DESCRIPTION

The present specification is based upon the production of modified cotton plants wherein the plants are modified using chimeric hairpin RNA gene-silencing constructs, Stable progeny are characterised by comprising oil having the highly desirable properties including significantly lower levels of palmitic acid and linoleic acid, and significantly higher levels of oleic acid than controls and than the levels that are typically found in cottonseed oil extracted from commercially useful cultivars of cotton. Reduced gene expression of CPA-FAS-2 facilitated a reduction in the level of cyclopropenoid fatty acids and the presence of CPA and/or CPE in cottonseed oil. Although the present invention is illustrated using hairpin RNA gene-silencing constructs, it is not so limited and other methods known to those of skill in the art such as those described herein are also contemplated for use in producing plants and products derived therefrom with the herein disclosed advantages.

Reference herein to cottonseed oil refers to endogenous cottonseed oil and cottonseed oil extracted from cottonseeds derived from the modified cotton plants described herein. Thus the present invention does not relate to post-extraction modification of cottonseed oil in a way that substantially alters the fatty acid composition.

The present invention involves modification of gene activity and the construction and use of chimeric genes. As used herein, the term “gene” includes any deoxyribonucleotide sequence which includes a protein coding region or which is transcribed in a cell but not translated, as well as associated non-coding and regulatory regions. Such associated regions are typically located adjacent to the coding region or the transcribed region on both the 5′ and 3′ ends for a distance of about 2 kb on either side. In this regard, the gene may include control signals such as promoters, enhancers, termination and/or polyadenylation signals that are naturally associated with a given gene, or heterologous control signals in which case the gene is referred to as a “chimeric gene”. The sequences which are located 5′ of the coding region and which are present on the mRNA are referred to as 5′ non-translated sequences. The sequences which are located 3′ or downstream of the coding region and which are present on the mRNA are referred to as 3′ non-translated sequences. The term “gene” encompasses both cDNA and genomic forms of a gene.

A “cotton FAD2-1 gene”, “ghFAD2-1 gene” or the like as used herein refers to a nucleotide sequence encoding oleoyl-Δ12-desaturase in cotton, which is expressed in developing cottonseed. A ghFAD2-1 gene can readily be distinguished from genes encoding other oleoyl-Δ12-desaturases or other proteins by those skilled in the art, in particular from a ghFAD2-2 gene, for example SEQ ID NO: 26. Cotton FAD2-1 genes include the naturally occurring alleles or variants existing in cotton, including those encoded by the A and D genomes of tetraploid cotton, as well as non-naturally occurring variants which may be produced by those skilled in the art of gene modification. An example of a naturally occurring variant of cotton ghFAD2-1 is the sequence shown herein as SEQ ID NO: 24, which has about 96% identity along its full length to SEQ ID NO: 1. In a preferred embodiment, a ghFAD2-1 gene refers to a nucleic acid molecule, which may be present in or isolated from cotton or derived therefrom, comprising nucleotides having a sequence having at least 90% identity to the protein coding region of the cDNA sequence shown in SEQ ID NO: 1.

A “cotton FatB-2 gene”, “ghFatB-2 gene” or the like as used herein refers to a nucleotide sequence encoding acyl-ACP thioesterase in cotton, which is expressed in developing cottonseed. A ghFatB-2 gene can readily be distinguished from genes encoding other acyl-ACP thioesterase or other proteins by those skilled in the art, in particular from a ghFatB-1, for example SEQ ID NO: 3, or from a ghFatB-3 gene, for example SEQ ID NO: 7. Cotton FatB-2 genes include the naturally occurring alleles or variants existing in cotton, including those encoded by the A and D genomes of tetraploid cotton, as well as non-naturally occurring variants which may be produced by those skilled in the art of gene modification. In a preferred embodiment, a ghFatB-2 gene refers to a nucleic acid molecule, which may be present in or isolated from cotton or derived therefrom, comprising nucleotides having a sequence having at least 90% identity to the protein coding region of the cDNA sequence shown in SEQ ID NO: 5.

A “cotton CPA-FAS-2 gene”, “ghCPA-FAS-2 gene” or the like as used herein refers to a nucleotide sequence encoding CPA fatty acid synthase in cotton, which is expressed in developing cottonseed. A ghCPA-FAS-2 gene can readily be distinguished from genes encoding other CPA fatty acid synthases or other proteins by those skilled in the art, in particular from a ghCPA-FAS-1, for example SEQ ID NO: 10, or from a ghCPA-FAS-3 gene, for example SEQ ID NO: 14. Cotton CPA-FAS-2 genes include the naturally occurring alleles or variants existing in cotton, including those encoded by the A and D genomes of tetraploid cotton, as well as non-naturally occurring variants which may be produced by those skilled in the art of gene modification. In a preferred embodiment, a ghCPA-FAS-2 gene refers to a nucleic acid molecule, which may be present in or isolated from cotton or derived therefrom, comprising nucleotides having a sequence having at least 90% identity to the protein coding region of the cDNA sequence shown in SEQ ID NO: 12.

A genomic form or clone of a gene containing the transcribed region may be interrupted with non-coding sequences termed “introns” or “intervening regions” or “intervening sequences.” An “intron” as used herein is a segment of a gene which is transcribed as part of a primary RNA transcript but is not present in the mature mRNA molecule. Introns are removed or “spliced out” from the nuclear or primary transcript; introns therefore are absent in the messenger RNA (mRNA). Introns may contain regulatory elements such as enhancers. “Exons” as used herein refer to the DNA regions corresponding to the RNA sequences which are present in the mature mRNA or the mature RNA molecule in cases where the RNA molecule is not translated. An mRNA functions during translation to specify the sequence or order of amino acids in a nascent polypeptide. The term “gene” includes a synthetic or fusion molecule encoding all or part of the proteins of the invention described herein and a complementary nucleotide sequence to any one of the above. A gene may be introduced into an appropriate vector for extrachromosomal maintenance in a cell or for integration into the host genome.

As used herein, a “chimeric gene” refers to any gene that is not a native gene in its native location. Typically a chimeric gene comprises regulatory and transcribed or protein coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. The term “endogenous” is used herein to refer to a substance that is normally present or produced in an unmodified plant at the same developmental stage as the plant under investigation. An “endogenous gene” refers to a native gene in its natural location in the genome of an organism. As used herein, “recombinant nucleic acid molecule” refers to a nucleic acid molecule which has been constructed or modified by recombinant DNA technology. The terms “foreign polynucleotide” or “exogenous polynucleotide” or “heterologous polynucleotide” and the like refer to any nucleic acid which is introduced into the genome of a cell by experimental manipulations. These include gene sequences found in that cell so long as the introduced gene contains some modification (e.g. a mutation, the presence of a selectable marker gene, etc.) relative to the naturally-occurring gene. Foreign or exogenous genes may be genes that are inserted into a non-native organism, native genes introduced into a new location within the native host, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure. The term “genetically modified” includes introducing genes into cells by transformation or transduction, mutating genes in cells and altering or modulating the regulation of a gene in a cell or organisms to which these acts have been done or their progeny.

Polynucleotides

The present invention refers to various polynucleotides. As used herein, a “polynucleotide” or “nucleic acid” or “nucleic acid molecule” means a polymer of nucleotides, which may be DNA or RNA or a combination thereof, and includes mRNA, cRNA, cDNA, tRNA, siRNA, shRNA and hpRNA. It may be DNA or RNA of cellular, genomic or synthetic origin, for example made on an automated synthesizer, and may be combined with carbohydrate, lipids, protein or other materials, labelled with fluorescent or other groups, or attached to a solid support to perform a particular activity defined herein, or comprise one or more modified nucleotides not found in nature, well known to those skilled in the art. The polymer may be single-stranded, essentially double-stranded or partly double-stranded. An example of a partly-double stranded RNA molecule is a hairpin RNA (hpRNA), short hairpin RNA (shRNA) or self-complementary RNA which include a double stranded stem formed by basepairing between a nucleotide sequence and its complement and a loop sequence which covalently joins the nucleotide sequence and its complement. Basepairing as used herein refers to standard basepairing between nucleotides, including G:U basepairs. “Complementary” means two polynucleotides are capable of basepairing (hybridizing) along part of their Lengths, or along the full length of one or both. A “hybridized polynucleotide” means the polynucleotide is actually basepaired to its complement. The term “polynucleotide” is used interchangeably herein with the term “nucleic acid”.

By “isolated” is meant material that is substantially or essentially free from components that normally accompany it in its native state. As used herein, an “isolated polynucleotide” or “isolated nucleic acid molecule” means a polynucleotide which is at least partially separated from, preferably substantially or essentially free of, the polynucleotide sequences of the same type with which it is associated or linked in its native state. For example, an “isolated polynucleotide” includes a polynucleotide which has been purified or separated from the sequences which flank it in a naturally occurring state, e.g., a DNA fragment which has been removed from the sequences which are normally adjacent to the fragment. Preferably, the isolated polynucleotide is also at least 90% free from other components such as proteins, carbohydrates, lipids etc. The term “recombinant polynucleotide” as used herein refers to a polynucleotide formed in vitro by the manipulation of nucleic acid into a form not normally found in nature. For example, the recombinant polynucleotide may be in the form of an expression vector. Generally, such expression vectors include transcriptional and translational regulatory nucleic acid operably connected to the nucleotide sequence.

The present invention refers to use of oligonucleotides. As used herein, “oligonucleotides” are polynucleotides up to 50 nucleotides in length. They can be RNA, DNA, or combinations or derivatives of either. Oligonucleotides are typically relatively short single stranded molecules of 10 to 30 nucleotides, commonly 15-25 nucleotides in length. When used as a probe or as a primer in an amplification reaction, the minimum size of such an oligonucleotide is the size required for the formation of a stable hybrid between the oligonucleotide and a complementary sequence on a target nucleic acid molecule. Preferably, the oligonucleotides are at least 15 nucleotides, more preferably at least 18 nucleotides, more preferably at least 19 nucleotides, more preferably at least 20 nucleotides, even more preferably at least 25 nucleotides in length.

Polynucleotides used as a probe are typically conjugated with a detectable label such as a radioisotope, an enzyme, biotin, a fluorescent molecule or a chemiluminescent molecule. Oligonucleotides of the invention are useful in methods of detecting an allele of an ghFAD2-1, ghFatB-2 and ghCPA-FAS-2 or other gene linked to a trait of interest, for example modified oil composition. Such methods, for example, employ nucleic acid hybridization and in many instances include oligonucleotide primer extension by a suitable polymerase (as used in PCR).

A variant of an oligonucleotide of the invention includes molecules of varying sizes of, and/or are capable of hybridising, for example, to the cotton genome close to that of, the specific oligonucleotide molecules defined herein. For example, variants may comprise additional nucleotides (such as 1, 2, 3, 4, or more), or less nucleotides as long as they still hybridise to the target region. Furthermore, a few nucleotides may be substituted without influencing the ability of the oligonucleotide to hybridise to the target region. In addition, variants may readily be designed which hybridise close to, for example to within 50 nucleotides, the region of the plant genome where the specific oligonucleotides defined herein hybridise.

The terms “polynucleotide variant” and “variant” and the like refer to polynucleotides or their complementary forms displaying substantial sequence identity with a reference polynucleotide sequence. These terms also encompass polynucleotides that are distinguished from a reference polynucleotide by the addition, deletion or substitution of at least one nucleotide. Accordingly, the terms “polynucleotide variant” and “variant” include polynucleotides in which one or more nucleotides have been added or deleted, or replaced with different nucleotides. In this regard, it is well understood in the art that certain alterations inclusive of mutations, additions, deletions and substitutions can be made to a reference polynucleotide whereby the altered polynucleotide retains the biological function or activity of the reference polynucleotide. Accordingly, these terms encompass polynucleotides that encode polypeptides that exhibit enzymatic or other regulatory activity, or polynucleotides capable of serving as selective probes or other hybridising agents. In particular, this includes polynucleotides which encode the same polypeptide or amino acid sequence but which vary in nucleotide sequence by redundancy of the genetic code. The terms “polynucleotide variant” and “variant” also include naturally occurring allelic variants.

By “corresponds to” or “corresponding to” is meant a polynucleotide (a) having a nucleotide sequence that is substantially identical or complementary to all or most of a reference polynucleotide sequence or (b) encoding an amino acid sequence identical to an amino acid sequence in a peptide or protein. This phrase also includes within its scope a peptide or polypeptide having an amino acid sequence that is substantially identical to a sequence of amino acids in a reference peptide or protein. Terms used to describe sequence relationships between two or more polynucleotides or polypeptides include “reference sequence”, “comparison window”, “sequence identity”, “percentage of sequence identity”, “substantial identity” and “identical”, and are defined with respect to a minimum number of nucleotides or amino acid residues or over the full length. The terms “sequence identity” and “identity” are used interchangeably herein to refer to the extent that sequences are identical on a nucleotide-by-nucleotide basis or an amino acid-by-amino acid basis over a window of comparison. Thus, a “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, U) or the identical amino acid residue (e.g., Ala, Pro, Ser. Thr, Gly, Val, Leu, Ile, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gln, Cys and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity.

The % identity of a polynucleotide can be determined by GAP (Needleman and Wunsch, J. Mol. Biol. 48: 443-453, 1970) analysis (GCG program) with a gap creation penalty=5, and a gap extension penalty=0.3. Unless stated otherwise, the query sequence is at least 45 nucleotides in length, and the GAP analysis aligns the two sequences over a region of at least 45 nucleotides. Preferably, the query sequence is at least 150 nucleotides in length, and the GAP analysis aligns the two sequences over a region of at least 150 nucleotides. More preferably, the query sequence is at least 300 nucleotides in length and the GAP analysis aligns the two sequences over a region of at least 300 nucleotides, or at least 400, at least 500 or at least 600 nucleotides in each case. Reference also may be made to the BLAST family of programs as for example disclosed by Altschul et al., Nucleic Acids Res. 25: 3389, 1997. A detailed discussion of sequence analysis can be found in Unit 19.3 of Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons Inc, 1994-1998, Chapter 15.

Nucleotide or amino acid sequences are indicated as “essentially similar” when such sequences have a sequence identity of at least 90%, especially at least 95%, more especially are identical. It is clear that when RNA sequences are described as essentially similar to, correspond to, or have a certain degree of sequence identity with, DNA sequences, thymine (T) in the DNA sequence is considered equal to uracil (U) in the RNA sequence.

With regard to the defined polynucleotides, it will be appreciated that % identity figures higher than those provided above will encompass preferred embodiments. Thus, where applicable, in light of the minimum % identity figures, it is preferred that the polynucleotide comprises a polynucleotide sequence which is at least 70%, preferably at least 80%, more preferably at least 85%, more preferably at least 90%, more preferably at least 91%, more preferably at least 92%, more preferably at least 93%, more preferably at least 94%, more preferably at least 95%, more preferably at least 96%, more preferably at least 97%, more preferably at least 98%, more preferably at least 99%, more preferably at least 99.1%, more preferably at least 99.2%, more preferably at least 99.3%, more preferably at least 99.4%, more preferably at least 99.5%, more preferably at least 99.6%, more preferably at least 99.7%, more preferably at least 99.8%, and even more preferably at least 99.9% identical to the relevant nominated SEQ CD NO.

Preferably, a polynucleotide of the invention which encodes a polypeptide with ghFAD2-1, ghFatB-2 or ghCPA-FAS-2 activity is greater than 800, preferably greater than 900, and even more preferably greater than 1,000 nucleotides in length.

Polynucleotides of the present invention may possess, when compared to naturally occurring molecules, one or more mutations which are deletions, insertions, or substitutions of nucleotide residues. Mutants can be either naturally occurring (that is to say, isolated from a natural source) or synthetic (for example, by performing site-directed mutagenesis on the nucleic acid).

The present invention refers to the stringency of hybridization conditions to define the extent of complementarity of two polynucleotides. “Stringency” as used herein, refers to the temperature and ionic strength conditions, and presence or absence of certain organic solvents, during hybridization and washing. The higher the stringency, the higher will be the degree of complementarity between a target nucleotide sequence and the labelled polynucleotide sequence (probe). “Stringent conditions” refers to temperature and ionic conditions under which only nucleotide sequences having a high frequency of complementary bases will hybridize. As used herein, the term “hybridizes under low stringency, medium stringency, high stringency, or very high stringency conditions” describes conditions for hybridization and washing Guidance for performing hybridization reactions can be found in Ausubel et al., (eds.), Current Protocols in Molecular Biology, John Wiley & Sons, NY, 6.3.1-6.3.6., 1989. Aqueous and nonaqueous methods are described in that reference and either can be used. Specific hybridization conditions referred to herein are as follows: 1) low stringency hybridization conditions are for hybridization in 6× sodium chloride/sodium citrate (SSC) at 45° C., followed by two washes in 0.2×SSC, 0.1% SDS at 50-55° C.; 2) medium stringency hybridization conditions are for hybridization in 6×SSC at about 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 60° C.; 3) high stringency hybridization conditions are for hybridization in 6×SSC at 45° C., followed by one or more washes in 0.2×SSC, 0.1% SDS at 65° C.; and 4) very high stringency hybridization conditions are for hybridization in 0.5 M sodium phosphate buffer, 7% SDS at 65° C., followed by one or more washes at 0.2×SSC, 1% SDS at 65° C.

Polypeptides

The terms “polypeptide” and “protein” are generally used interchangeably. The terms “proteins” and “polypeptides” as used herein also include variants, mutants, modifications, analogs and/or derivatives of the polypeptides of the invention as described herein. As used herein, “substantially purified polypeptide” refers to a polypeptide that has been separated from the lipids, nucleic acids, other peptides and other molecules with which it is associated in its native state. Preferably, the substantially purified polypeptide is at least 90% free from other components with which it is naturally associated. By “recombinant polypeptide” is meant a polypeptide made using recombinant techniques, i.e., through the expression of a recombinant polynucleotide in a cell, preferably a plant cell and more preferably a cereal plant cell.

The % identity of a polypeptide relative to another polypeptide can be determined by GAP (Needleman and Wunsch, 1970 (supra)) analysis (GCG program) with a gap creation penalty=5, and a gap extension penalty=0.3. The query sequence is at least 15 amino acids in length, and the GAP analysis aligns the two sequences over a region of at least 15 amino acids. More preferably, the query sequence is at least 50 amino acids in length, and the GAP analysis aligns the two sequences over a region of at least 50 amino acids. More preferably, the query sequence is at least 100 amino acids in length and the GAP analysis aligns the two sequences over a region of at least 100 amino acids. Even more preferably, the query sequence is at least 250 amino acids in length and the GAP analysis aligns the two sequences over a region of at least 250 amino acids.

As used herein a “biologically active” fragment of a polypeptide is a portion of a polypeptide of the invention, less than full length, which maintains a defined activity of the full-length polypeptide. Biologically active fragments can be any size as long as they maintain the defined activity, but are preferably at least 200 or at least 250 amino acid residues long.

With regard to a defined polypeptide, it will be appreciated that % identity figures higher than those provided above will encompass preferred embodiments. Thus, where applicable, in light of the minimum % identity figures, it is preferred that the polypeptide comprises an amino acid sequence which is at least 80%, more preferably at least 85%, more preferably at least 90%, more preferably at least 91%, more preferably at least 92%, more preferably at least 93%, more preferably at least 94%, more preferably at least 95%, more preferably at least 96%, more preferably at least 97%, more preferably at least 98%, more preferably at least 99%, more preferably at least 99.1%, more preferably at least 99.2%, more preferably at least 99.3%, more preferably at least 99.4%, more preferably at least 99.5%, more preferably at least 99.6%, more preferably at least 99.7%, more preferably at least 99.8%, and even more preferably at least 99.9% identical to the relevant nominated SEQ ID NO.

Amino acid sequence mutants of the polypeptides of the present invention can be prepared by introducing appropriate nucleotide changes into a nucleic acid of the present invention, or by in vitro synthesis of the desired polypeptide. Such mutants include, for example, deletions, insertions or substitutions of residues within the amino acid sequence. A combination of deletion, insertion and substitution can be made to arrive at the final construct, provided that the final peptide product possesses the desired characteristics.

Mutant (altered) peptides can be prepared using any technique known in the art. For example, a polynucleotide of the invention can be subjected to in vitro mutagenesis. Such in vitro mutagenesis techniques include sub-cloning the polynucleotide into a suitable vector, transforming the vector into a “mutator” strain such as the E. coli XL-1 red (Stratagene) and propagating the transformed bacteria for a suitable number of generations. In another example, the polynucleotides of the invention are subjected to DNA shuffling techniques as broadly described by Harayama, Trends Biotechnol. 16: 76-82, 1998. These DNA shuffling techniques may include genes related to those of the present invention, such as genes from plant species other than cotton, and/or include different genes from the same plant encoding similar proteins. Products derived from mutated/altered DNA can readily be screened using techniques described herein to determine if they possess, for example, FAD2 activity.

In designing amino acid sequence mutants, the location of the mutation site and the nature of the mutation will depend on characteristic(s) to be modified. The sites for mutation can be modified individually or in series, e.g., by (1) substituting first with conservative amino acid choices and then with more radical selections depending upon the results achieved, (2) deleting the target residue, or (3) inserting other residues adjacent to the located site.

Amino acid sequence deletions generally range from about 1 to 15 residues, more preferably about 1 to 10 residues and typically about 1 to 5 contiguous residues.

Substitution mutants have at least one amino acid residue in the polypeptide molecule removed and a different residue inserted in its place. The sites of greatest interest for substitutional mutagenesis include sites identified as the active site(s). Other sites of interest are those in which particular residues obtained from various strains or species are identical. These positions may be important for biological activity. These sites, especially those falling within a sequence of at least three other identically conserved sites, are preferably substituted in a relatively conservative manner. Such conservative substitutions are shown in Table 5 under the heading of “exemplary substitutions”.

Polypeptides of the present invention can be produced in a variety of ways, including production and recovery of natural polypeptides, and production and recovery of recombinant polypeptides. In one embodiment, an isolated polypeptide of the present invention is produced by culturing a cell capable of expressing the polypeptide under conditions effective to produce the polypeptide, and recovering the polypeptide. A preferred cell to culture is a recombinant cell of the present invention.

The present invention refers to elements which are operably connected or linked. “Operably connected” or “operably linked” and the like refer to a linkage of polynucleotide elements in a functional relationship. Typically, operably connected nucleic acid sequences are contiguously linked and, where necessary to join two protein coding regions, contiguous and in reading frame. A coding sequence is “operably connected to” another coding sequence when RNA polymerase will transcribe the two coding sequences into a single RNA, which if translated is then translated into a single polypeptide having amino acids derived from both coding sequences. The coding sequences need not be contiguous to one another so long as the expressed sequences are ultimately processed to produce the desired protein.

As used herein, the term “cis-acting sequence”, “cis-acting element” or “cis-regulatory region” or “regulatory region” or similar term shall be taken to mean any sequence of nucleotides, which when positioned appropriately and connected relative to an expressible genetic sequence, is capable of regulating, at least in part, the expression of the genetic sequence. Those skilled in the art will be aware that a cis-regulatory region may be capable of activating, silencing, enhancing, repressing or otherwise altering the level of expression and/or cell-type-specificity and/or developmental specificity of a gene sequence at the transcriptional or post-transcriptional level. In certain embodiments of the present invention, the cis-acting sequence is an activator sequence that enhances or stimulates the expression of an expressible genetic sequence.

“Operably connecting” a promoter or enhancer element to a transcribable polynucleotide means placing the transcribable polynucleotide (e.g., protein-encoding polynucleotide or other transcript) under the regulatory control of a promoter, which then controls the transcription of that polynucleotide. In the construction of heterologous promoter/structural gene combinations, it is generally preferred to position a promoter or variant thereof at a distance from the transcription start site of the transcribable polynucleotide which is approximately the same as the distance between that promoter and the protein coding region it controls in its natural setting; i.e., the gene from which the promoter is derived. As is known in the art, some variation in this distance can be accommodated without loss of function. Similarly, the preferred positioning of a regulatory sequence element (e.g., an operator, enhancer etc) with respect to a transcribable polynucleotide to be placed under its control is defined by the positioning of the element in its natural setting; i.e., the genes from which it is derived.

“Promoter” or “promoter sequence” as used herein refers to a region of a gene, generally upstream (5′) of the RNA encoding region, which controls the initiation and level of transcription in the cell of interest. A “promoter” includes the transcriptional regulatory sequences of a classical genomic gene, including a TATA box and CCAAT box sequences, as well as additional regulatory elements (i.e., upstream activating sequences, enhancers and silencers) that alter gene expression in response to developmental and/or environmental stimuli, or in a tissue-specific or cell-type-specific manner. A promoter is usually, but not necessarily (for example, some PolIII promoters), positioned upstream of a structural gene, the expression of which it regulates. Furthermore, the regulatory elements comprising a promoter are usually positioned within 2 kb of the start site of transcription of the gene. Promoters may contain additional specific regulatory elements, located more distal to the start site to further enhance expression in a cell, and/or to alter the timing or inducibility of expression of a structural gene to which it is operably connected.

“Constitutive promoter” refers to a promoter that directs expression of an operably linked transcribed sequence in many or all tissues of a plant. The term constitutive as used herein does not necessarily indicate that a gene is expressed at the same level in all cell types, but that the gene is expressed in a wide range of cell types, although some variation in level is often detectable. “Selective expression” as used herein refers to expression almost exclusively in specific organs of the plant, such as, for example, endosperm, embryo, leaves, fruit, tubers or root. In a preferred embodiment, a promoter is expressed selectively or preferentially in developing seed of a plant, preferably a cotton plant. The term may also refer to expression at specific developmental stages in an organ, such as in early, mid or late embryogenesis or different stages of maturity, or to expression that is inducible by certain environmental conditions or treatments. Selective expression may therefore be contrasted with constitutive expression, which refers to expression in many or all tissues of a plant under most or all of the conditions experienced by the plant.

Selective expression may also result in compartmentation of the products of gene expression in specific plant tissues, organs or developmental stages. Compartmentation in specific subcellular locations such as the plastid, cytosol, vacuole, or apoplastic space may be achieved by the inclusion in the structure of the gene product of appropriate signals, eg. a signal peptide, for transport to the required cellular compartment, or in the case of the semi-autonomous organelles (plastids and mitochondria) by integration of the transgene with appropriate regulatory sequences directly into the organelle genome.

A “tissue-specific promoter” or “organ-specific promoter” is a promoter that is preferentially expressed in one tissue or organ relative to many other tissues or organs, preferably most if not all other tissues or organs in a plant. Typically, the promoter is expressed at a level 10-fold higher in the specific tissue or organ than in other tissues or organs. An illustrative tissue specific promoter is the promoter from a lectin gene (SEQ ID NO: 16) which is expressed preferentially in the developing seed of dicot plants such as cotton. Other seed specific promoters are well known in the art.

The promoters contemplated by the present invention may be native to the host plant to be transformed or may be derived from an alternative source, where the region is functional in the host plant. Other sources include the Agrobacterium T-DNA genes, such as the promoters of genes for the biosynthesis of nopaline, octapine, mannopine, or other opine promoters, tissue specific promoters (see, e.g., U.S. Pat. No. 5,459,252 to Conkling et al.; WO 91/13992 to Advanced Technologies); promoters from viruses (including host specific viruses), or partially or wholly synthetic promoters. Numerous promoters that are functional in mono- and dicotyledonous plants are well known in the art (see, for example, Greve, J. Mol. Appl. Genet., 1: 499-511, 1983; Salomon et al., EMBO J., 3: 141-146, 1984; Garfinkel et al., Cell, 27: 143-153, 1983; Barker et al., Plant Mol. Biol., 2: 235-350, 1983; including various promoters isolated from plants and viruses such as the cauliflower mosaic virus promoter (CaMV 35S, 19S). Many tissue specific promoter regions are known. Other transcriptional initiation regions which preferentially provide for transcription in certain tissues or under certain growth conditions, include those from genes encoding napin, seed ACP, zein, or other seed storage proteins. Non-limiting methods for assessing promoter activity are disclosed by Medberry et al., Plant Cell, 4: 185-192, 1992, Medberry et al., Plant J. 3: 619-626, 1993, Sambrook et al., Molecular Cloning: A Laboratory Manual (2nd Ed). Cold Spring Harbour Laboratory, Cold Spring Harbour, N.Y. 1989 and McPherson et al., (U.S. Pat. No. 5,164,316).

Alternatively or additionally, the promoter may be an inducible promoter or a developmentally regulated promoter which is capable of driving expression of the introduced polynucleotide at an appropriate developmental stage of the plant. Other cis-acting sequences which may be employed include transcriptional and/or translational enhancers. Enhancer regions are well known to persons skilled in the art, and can include an ATG translational initiation codon and adjacent sequences. When included, the initiation codon should be in phase with the reading frame of the coding sequence relating to the foreign or exogenous polynucleotide to ensure translation of the entire sequence if it is to be translated. Translational initiation regions may be provided from the source of the transcriptional initiation region, or from a foreign or exogenous polynucleotide. The sequence can also be derived from the source of the promoter selected to drive transcription, and can be specifically modified so as to increase translation of the mRNA.

The nucleic acid construct of the present invention may comprise a 3′ non-translated sequence from about 50 to 1,000 nucleotide base pairs which may include a transcription termination sequence. A 3′ non-translated sequence may contain a transcription termination signal which may or may not include a polyadenylation signal and any other regulatory signals capable of effecting mRNA processing. A polyadenylation signal functions for addition of polyadenylic acid tracts to the 3′ end of a mRNA precursor. Polyadenylation signals are commonly recognized by the presence of homology to the canonical form 5′ AATAAA-3′ although variations are not uncommon. Transcription termination sequences which do not include a polyadenylation signal include terminators for PolI or PolIII RNA polymerase which comprise a run of four or more thymidines. Examples of suitable 3′ non-translated sequences are the 3′ transcribed non-translated regions containing a polyadenylation signal from a lectin gene (SEQ ID NO: 20), the S3 gene of Subclover Stunt Virus (SEQ ID NO: 23), or nopaline synthase (nos) gene of Agrobacterium tumefaciens (Bevan et al., Nucl. Acid Res., 11: 369, 1983). Suitable 3′ non-translated sequences may also be derived from plant genes such as the 3′ end of the protease inhibitor I or II genes from potato or tomato, the soybean storage protein genes and the small subunit of the ribulose-1,5-bisphosphate carboxylase (ssRUBISCO) gene, although other 3′ elements known to those of skill in the art can also be employed.

As the DNA sequence inserted between the transcription initiation site and the start of the coding sequence, i.e., the untranslated 5′ leader sequence (5′UTR), can influence gene expression if it is translated as well as transcribed, one can also employ a particular leader sequence. Suitable leader sequences include those that comprise sequences selected to direct optimum expression of the foreign or endogenous DNA sequence. For example, such leader sequences include a preferred consensus sequence which can increase or maintain mRNA stability and prevent inappropriate initiation of translation as for example described by Joshi, Nucl. Acid Res. 15: 6643, 1987.

Additionally, targeting sequences may be employed to target the enzyme encoded by the foreign or exogenous polynucleotide to an intracellular compartment, for example to the chloroplast, within plant cells or to the extracellular environment. For example, a nucleic acid sequence encoding a transit or signal peptide sequence may be operably linked to a sequence that encodes a chosen enzyme of the subject invention such that, when translated, the transit or signal peptide can transport the enzyme to a particular intracellular or extracellular destination, and can then be optionally post-translationally removed. Transit or signal peptides act by facilitating the transport of proteins through intracellular membranes, e.g., endoplasmic reticulum, vacuole, vesicle, plastid, mitochondrial and plasmalemma membranes. For example, the targeting sequence can direct a desired protein to a particular organelle such as a vacuole or a plastid (e.g., a chloroplast), rather than to the cytosol. Thus, the nucleic acid construct of the invention can further comprise a plastid transit peptide-encoding nucleic acid sequence operably linked between a promoter region and the foreign or exogenous polynucleotide. Sequences encoding such signal peptides are often found in naturally occurring genes and may be employed, such as, for example, in the ghFatB genes described herein.

Vectors

The present invention includes use of vectors for manipulation or transfer of genetic constructs. By “vector” is meant a nucleic acid molecule, preferably a DNA molecule derived, for example, from a plasmid, bacteriophage, or plant virus, into which a nucleic acid sequence may be inserted or cloned. A vector preferably is double-stranded DNA and contains one or more unique restriction sites and may be capable of autonomous replication in a defined host cell including a target cell or tissue or a progenitor cell or tissue thereof, or capable of integration into the genome of the defined host such that the cloned sequence is reproducible. Accordingly, the vector may be an autonomously replicating vector, i.e., a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a linear or closed circular plasmid, an extrachromosomal element, a minichromosome, or an artificial chromosome. The vector may contain any means for assuring self-replication. Alternatively, the vector may be one which, when introduced into a cell, is integrated into the genome of the recipient cell and replicated together with the chromosome(s) into which it has been integrated. A vector system may comprise a single vector or plasmid, two or more vectors or plasmids, which together contain the total DNA to be introduced into the genome of the host cell, or a transposon. The choice of the vector will typically depend on the compatibility of the vector with the cell into which the vector is to be introduced. The vector may also include a selection marker such as an antibiotic resistance gene, a herbicide resistance gene or other gene that can be used for selection of suitable transformants. Examples of such genes are well known to those of skill in the art.

The nucleic acid construct of the invention can be introduced into a vector, such as a plasmid. Plasmid vectors typically include additional nucleic acid sequences that provide for easy selection, amplification, and transformation of the expression cassette in prokaryotic and eukaryotic cells, e.g., pUC-derived vectors, pSK-derived vectors, pGEM-derived vectors, pSP-derived vectors, pBS-derived vectors, or binary vectors containing one or more T-DNA regions. Additional nucleic acid sequences include origins of replication to provide for autonomous replication of the vector, selectable marker genes, preferably encoding antibiotic or herbicide resistance, unique multiple cloning sites providing for multiple sites to insert nucleic acid sequences or genes encoded in the nucleic acid construct, and sequences that enhance transformation of prokaryotic and eukaryotic (especially plant) cells.

By “marker gene” is meant a gene that imparts a distinct phenotype to cells expressing the marker gene and thus allows such transformed cells to be distinguished from cells that do not have the marker. A selectable marker gene confers a trait for which one can “select” based on resistance to a selective agent (e.g., a herbicide, antibiotic, radiation, heat, or other treatment damaging to untransformed cells). A screenable marker gene (or reporter gene) confers a trait that one can identify through observation or testing, i.e., by “screening” (e.g., β-glucuronidase, luciferase, GFP or other enzyme activity not present in untransformed cells). The marker gene and the nucleotide sequence of interest do not have to be linked. An example of a selectable marker gene is the S1-NptII-S3 terminator gene shown schematically in FIG. 12, comprising SEQ ID NOs: 21-23.

To facilitate identification of transformants, the nucleic acid construct desirably comprises a selectable or screenable marker gene as, or in addition to, the foreign or exogenous polynucleotide. The actual choice of a marker is not crucial as long as it is functional (i.e., selective) in combination with the plant cells of choice. The marker gene and the foreign or exogenous polynucleotide of interest do not have to be linked, since co-transformation of unlinked genes as, for example, described in U.S. Pat. No. 4,399,216 is also an efficient process in plant transformation.

Examples of bacterial selectable markers are markers that confer antibiotic resistance such as ampicillin, erythromycin, chloramphenicol or tetracycline resistance, preferably kanamycin resistance. Exemplary selectable markers for selection of plant transformants include, but are not limited to, a hyg gene which encodes hygromycin B resistance; a neomycin phosphotransferase (nptII) gene conferring resistance to kanamycin, paromomycin, G418; a glutathione-S-transferase gene from rat liver conferring resistance to glutathione derived herbicides as, for example, described in EP-A 256223; a glutamine synthetase gene conferring, upon overexpression, resistance to glutamine synthetase inhibitors such as phosphinothricin as, for example, described in WO87/05327, an acetyltransferase gene from Streptomyces viridochromogenes conferring resistance to the selective agent phosphinothricin as, for example, described in EP-A 275957, a gene encoding a 5-enolshikimate-3-phosphate synthase (EPSPS) conferring tolerance to N-phosphonomethylglycine as, for example, described by Hinchee et al., Biotech. 6: 915, 1988, a bar gene conferring resistance against bialaphos as, for example, described in WO91/02071; a nitrilase gene such as bin from Klebsiella ozaenae which confers resistance to bromoxynil (Stalker et al., Science, 242: 419, 1988); a dihydrofolate reductase (DHFR) gene conferring resistance to methotrexate (Thillet et al., J. Biol. Chem. 263: 12500, 1988); a mutant acetolactate synthase gene (ALS), which confers resistance to imidazolinone, sulfonylurea or other ALS-inhibiting chemicals (EP-A-154 204); a mutated anthranilate synthase gene that confers resistance to 5-methyl tryptophan; or a dalapon dehalogenase gene that confers resistance to the herbicide.

Preferred screenable markers include, but are not limited to, a uidA gene encoding a β-glucuronidase (GUS) enzyme for which various chromogenic substrates are known, a β-galactosidase gene encoding an enzyme for which chromogenic substrates are known, an aequorin gene (Prasher et al., Biochem. Biophys. Res. Comm. 126: 1259-68, 1985), which may be employed in calcium-sensitive bioluminescence detection; a green fluorescent protein gene (Niedz et al., Plant Cell Reports, 14: 403, 1995.) or derivatives thereof; a luciferase (luc) gene (Ow et al., Science, 234: 856, 1986), which allows for bioluminescence detection, and others known in the art. By “reporter molecule” as used in the present specification is meant a molecule that, by its chemical nature, provides an analytically identifiable signal that facilitates determination of promoter activity by reference to protein product.

Methods of Modifying Gene Expression

The level of a protein, for example an enzyme involved in oil biosynthesis in developing seeds of a plant, may be modulated by increasing the level of expression of a nucleotide sequence that codes for the protein in a plant cell, or decreasing the level of expression of a gene encoding the protein in the plant, leading to modified oil composition in the mature seed. The level of expression of a gene may be modulated by altering the copy number per cell, for example by introducing a synthetic genetic construct comprising the coding sequence and a transcriptional control element that is operably connected thereto and that is functional in the cell. A plurality of transformants may be selected and screened for those with a favourable level and/or specificity of transgene expression arising from influences of endogenous sequences in the vicinity of the transgene integration site. A favourable level and pattern of transgene expression is one which results in a substantial modification of oil composition. This may be detected by simple testing of seedoil from the transformants. Alternatively, a population of mutagenized grain or a population of plants from a breeding program may be screened for individual lines with altered oil content or composition.

Reducing gene expression may be achieved through introduction and transcription of a “gene-silencing chimeric gene” introduced into the plant cell. The gene-silencing chimeric gene may be introduced stably into the plant cell's genome, preferably nuclear genome, or it may be introduced transiently, for example on a viral vector. As used herein “gene-silencing effect” refers to the reduction of expression of a target nucleic acid in a plant cell, which can be achieved by introduction of a silencing RNA. Such reduction may be the result of reduction of transcription, including via methylation of chromatin remodeling, or post-transcriptional modification of the RNA molecules, including via RNA degradation, or both. Gene-silencing includes an abolishing of the expression of the target nucleic acid or gene and a partial effect in either extent or duration. It is sufficient that the level of expression of the target nucleic acid in the presence of the silencing RNA is lower that in the absence thereof. The level of expression may be reduced by at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90%, or at least about 95%, or at least about 99%. In preferred embodiments, the expression of the cotton ghCPA-FAS-2 gene is reduced in seed by at least 60%, more preferably by at least 80% relative to a corresponding seed lacking the gene-silencing chimeric DNA. The target nucleic acid may be a gene involved in oil biosynthesis, oil accumulation such as genes involved in TAG assembly, including but not limited to acyltransferases or other enzymes of the Kennedey pathway, or oil metabolism, or may be any other endogenous genes, transgenes or exogenous genes such as viral genes which may not be present in the plant cell at the time of introduction of the transgene. In some embodiment the specification provides a method of modifying the endogenous oil of a cotton plant comprising producing a transgenic cotton plant having a gene construct which comprises a nucleotide sequence of a fatty acid biosynthesis gene or a gene fragment thereof, wherein said gene or gene fragment is placed operably in connection with a promoter sequence capable of conferring expression of said gene or gene fragment in the seed of a cotton plant, and wherein said fatty acid biosynthesis gene is two or more of FAD2 desaturase, FatB thioesterase, and CPA-FAS-2 fatty acid synthase. As described herein, reduction in gene expression improves the fatty acid content of endogenous and extractedoil.

Antisense RNA Molecules

Antisense techniques may be used to reduce gene expression according to the invention. The term “antisense RNA” shall be taken to mean an RNA molecule that is complementary to at least a portion of a specific mRNA molecule and capable of reducing expression of the gene encoding the mRNA. Such reduction typically occurs in a sequence-dependent manner and is thought to occur by interfering with a post-transcriptional event such as mRNA transport from nucleus to cytoplasm, mRNA stability or inhibition of translation. The use of antisense methods is well known in the art (see for example, Hartmann and Endres, Manual of Antisense Methodology, Kluwer, 1999). The use of antisense techniques in plants has been reviewed by Bourque, Plant Science, 105: 125-149, 1995 and Senior, Biotech. Genet. Engin. Revs. 15: 79-119, 1998. Bourque, 1995 (supra) lists a large number of examples of how antisense sequences have been utilized in plant systems as a method of gene inactivation. She also states that attaining 100% inhibition of any enzyme activity may not be necessary as partial inhibition will more than likely result in measurable change in the system. Senior, 1998 (supra) states that antisense methods are now a very well established technique for manipulating gene expression.

As used herein, the term “an antisense polynucleotide which hybridises under physiological conditions” means that the polynucleotide (which is fully or partially single stranded) is at least capable of forming a double stranded polynucleotide with an RNA product of the gene to be inhibited, typically the mRNA encoding a protein such as those provided herein, under normal conditions in a cell. Antisense molecules may include sequences that correspond to the structural genes or for sequences that effect control over the gene expression or splicing event. For example, the antisense sequence may correspond to the coding region of the targeted gene, or the 5′-untranslated region (UTR) or the 3′-UTR or combination of these. It may be complementary in part to intron sequences, which may be spliced out during or after transcription, but is preferably complementary only to exon sequences of the target gene. In view of the generally greater divergence of the UTRs, targeting these regions provides greater specificity of gene inhibition.

The length of the antisense sequence should be at least 19 contiguous nucleotides, preferably at least 25 or 30 or 50 nucleotides, and more preferably at least 100, 200, 500 or 1000 nucleotides, to a maximum of the full length of the gene to be inhibited. The full-length sequence complementary to the entire gene transcript may be used. The length is most preferably 100-2000 nucleotides. The degree of identity of the antisense sequence to the targeted transcript should be at least 90% and more preferably 95-100%. Preferred antisense sequences comprise at least 30 contiguous nucleotides which are the complement of any sequence of at least 30 contiguous nucleotides from SEQ ID NOs: 1, 5, or 12. The antisense RNA molecule may of course comprise unrelated sequences which may function to stabilize the molecule.

Genetic constructs to express an antisense RNA may be readily made by joining a promoter sequence to a region of the target gene in an “antisense” orientation, which as used herein refers to the reverse orientation relative to the orientation of transcription and translation (if it occurs) of the sequence in the target gene in the plant cell. Accordingly, also provided by this invention is a nucleic acid molecule such as a chimeric DNA coding for an antisense RNA of the invention, including cells, tissues, organs, plants, seeds, particularly cotton plants or cottonseed and the like comprising the nucleic acid molecule.

Ribozymes

The term “ribozyme” as used herein refers to an RNA molecule which specifically recognizes a distinct substrate RNA and catalyzes its cleavage. Typically, the ribozyme contains a region of nucleotides which are complementary to a region of the target RNA, enabling the ribozyme to specifically hybridize to the target RNA under physiological conditions, for example in the cell in which the ribozyme acts, and an enzymatic region referred to herein as the “catalytic domain”. The types of ribozymes that are particularly useful in this invention are the hammerhead ribozyme (Haseloff and Gerlach, Nature 334: 585-591, 1988, Perriman et al., Gene, 113: 157-163, 1992) and the hairpin ribozyme (Shippy et al., Mol. Biotech. 12: 117-129, 1999). DNA encoding the ribozymes can be synthesized using methods well known in the art and may be incorporated into a genetic construct or expression vector for expression in the cell of interest. Accordingly, also provided by this invention is a nucleic acid molecule such as a chimeric DNA coding for a ribozyme of the invention, including cells, tissues, organs, plants, grain and the like comprising the nucleic acid molecule. Typically, the DNA encoding the ribozyme is inserted into an expression cassette under control of a promoter and a transcription termination signal that function in the cell. Specific ribozyme cleavage sites within any potential RNA target may be identified by scanning the target molecule for ribozyme cleavage sites which include the trinucleotide sequences GUA, GUU and GUC. Once identified, short RNA sequences of between about 5 and 20 ribonucleotides corresponding to the region of the target gene 5′ and 3′ of the cleavage site may be evaluated for predicted structural features such as secondary structure that may render the oligonucleotide sequence less suitable. When employed, ribozymes may be selected from the group consisting of hammerhead ribozymes, hairpin ribozymes, axehead ribozymes, newt satellite ribozymes, Tetrahymena ribozymes and RNAse P ribozymes, and are designed according to methods known in the art based on the sequence of the target gene (for instance, see U.S. Pat. No. 5,741,679). The suitability of candidate targets may also be evaluated by testing their accessibility to hybridization with complementary oligonucleotides, using ribonuclease protection assays.

As with antisense polynucleotides described herein, ribozymes of the invention should be capable of hybridizing to a target nucleic acid molecule (for example SEQ ID NOs: 1, 5 or 12) under “physiological conditions”, namely those conditions within a cell, especially conditions in a plant cell such as a wheat or barley cell.

RNA Interference/Duplex RNA

As used herein, “artificially introduced dsRNA molecule” refers to the introduction of dsRNA molecule, which may be produced in the cell by transcription from a chimeric gene encoding such dsRNA molecule, however does not refer to the conversion Of a single stranded RNA molecule into a dsRNA inside the eukaryotic cell or plant cell. RNA interference (RNAi) is particularly useful for specifically reducing the expression of a gene or inhibiting the production of a particular protein. Although not wishing to be limited by theory, Waterhouse et al., Proc. Natl. Acad. Sci. U.S.A. 95: 13959-13964, 1998 have provided a model for the mechanism by which dsRNA can be used to reduce gene expression or protein production. This technology relies on the presence of dsRNA molecules that contain a sequence that is essentially identical to the mRNA of the gene of interest or part thereof. Conveniently, the dsRNA can be produced from a single promoter in a recombinant vector or host cell, where the sense and anti-sense sequences are transcribed to produce a hairpin RNA in which the sense and anti-sense sequences hybridize to form the dsRNA region with an intervening sequence or spacer region forming a loop structure, so the hairpin RNA comprises a stem-loop structure. The design and production of suitable dsRNA molecules for the present invention is well within the capacity of a person skilled in the art, particularly considering Waterhouse et al., 1998 (supra), Smith et al., Nature, 407: 319-320, 2000, WO 99/53050, WO 99/49029, and WO 01/34815. Accordingly, also provided by this invention is a nucleic acid molecule such as a chimeric DNA coding for a duplex RNA such as a hairpin RNA of the invention, including cells, tissues, organs, plants, seeds, particularly cotton plants or cottonseed, and the like comprising the nucleic acid molecule. In a preferred embodiment, the chimeric DNA has the structure shown schematically in FIG. 12, comprising the sequence shown in FIG. 13, referred to herein as the MonoCott construct.

In one example, a DNA is introduced that directs the synthesis of an at least partly double stranded RNA product(s) with homology to the target gene to be inactivated. The DNA therefore comprises both sense and antisense sequences that, when transcribed into RNA, can hybridize to form the double-stranded RNA region. In a preferred embodiment, the sense and antisense sequences are separated by a spacer region that comprises an intron which, when transcribed into RNA, is spliced out. A preferred intron is an intron from the ghFAD2-1 gene, for example SEQ ID NO: 18. This arrangement has been shown to result in a higher efficiency of gene silencing (Smith et al., 2000 (supra)). The double-stranded region may comprise one or two RNA molecules, transcribed from either one DNA region or two. The dsRNA may be classified as long hpRNA, having long, sense and antisense regions which can be largely complementary, but need not be entirely complementary (typically forming a basepaired region larger than about 100 bp, preferably ranging between 200-1000 bp). hpRNA can also be smaller with the double-stranded portion ranging in size from about 30 to about 50 bp, or from 30 to about 100 bp (see WO04/073390, herein incorporated by reference). The presence of the double stranded RNA region is thought to trigger a response from an endogenous plant system that processes the double stranded RNA to oligonucleotides of 21-24 nucleotides long, and also uses these oligonucleotides for sequence-specific cleavage of the homologous RNA transcript from the target plant gene, efficiently reducing or eliminating the activity of the target gene.

The length of the sense and antisense sequences that hybridise should each be at least 19 contiguous nucleotides, preferably at least 27 or 30 or 50 nucleotides, and more preferably at least 100, 200, or 500 nucleotides, up to the full-length sequence corresponding to the entire gene transcript. The lengths are most preferably 100-2000 nucleotides. The degree of identity of the sense and antisense sequences to the targeted transcript should be at least 85%, preferably at least 90% and more preferably 95-100%. The longer the sequence, the less stringent the requirement is for overall sequence identity. The RNA molecule may of course comprise unrelated sequences which may function to stabilize the molecule. The RNA molecule may be a hybrid between different sequences targeting different target RNAs, allowing reduction in expression of more than one target gene, or it may be one sequence which corresponds to a family of related target genes such as a multigene family. In a preferred embodiment, the RNA molecule targets at least three different target genes, more preferably the ghFAD2-1, ghFatB-2 and ghCPA-FAS-2 genes in cotton. The sequences used in the dsRNA preferably correspond to exon sequences of the target gene and may correspond to 5′ and/or 3′ untranslated sequences or protein coding sequences or any combination thereof. The promoter used to express the dsRNA-forming construct may be any type of promoter if the resulting dsRNA is specific for a gene product in the cell lineage targeted for destruction. Alternatively, the promoter may be lineage specific in that it is only expressed in cells of a particular development lineage. This might be advantageous where some overlap in homology is observed with a gene that is expressed in a non-targeted cell lineage. The promoter may also be inducible by externally controlled factors, or by intracellular environmental factors. Typically, the RNA molecule is expressed under the control of a RNA polymerase II or RNA polymerase III promoter. Examples of the latter include tRNA or snRNA promoters.

Examples of genetic constructs that encode dsRNA molecules that may be used to down-regulate the production of polypeptides for modification of oil composition in cottonseed are provided in Example 5.

Other silencing RNA may be “unpolyadenylated RNA” comprising at least 20 consecutive nucleotides having at least 95% sequence identity to the complement of a nucleotide sequence of an RNA transcript of the target gene, such as described in WO01/12824 or U.S. Pat. No. 6,423,885 (both documents herein incorporated by reference). Yet another type of silencing RNA is an RNA molecule as described in WO03/076619 (herein incorporated by reference) comprising at least 20 consecutive nucleotides having at least 95% sequence identity to the sequence of the target nucleic acid or the complement thereof, and further comprising a largely-double stranded region as described in WO03/076619.

MicroRNA regulation is a specialized branch of the RNA silencing pathway that evolved towards gene regulation, diverging from conventional RNAi/PTGS. MicroRNAs are a specific class of small RNAs that are encoded in gene-like elements organized in a characteristic partial inverted repeat. When transcribed, microRNA genes give rise to partially basepaired stem-looped precursor RNAs from which the microRNAs are subsequently processed. Processed microRNAs are typically 21 contiguous nucleotides in length or 21-23 nucleotides in length which are at least 95% identical in sequence to 21 contiguous nucleotides of the complement of the RNA transcript of the target gene. The released miRNAs are incorporated into RISC-like complexes containing a particular subset of Argonaute proteins that exert sequence-specific gene repression (see, for example, Millar and Waterhouse, Funct Integr Genomics, 5: 129-135, 2005; Pasquinelli et al., Curr Opin Genet Develop 15: 200-205, 2005; Almeida and Allshire, Trends Cell Biol. 15: 251-258, 2005, herein incorporated by reference).

Cosuppression

Another molecular biological approach that may be used for specifically reducing gene expression is co-suppression. The mechanism of co-suppression is not well understood but is thought to involve post-transcriptional gene silencing (PTGS) and in that regard may be very similar to many examples of antisense suppression. It involves introducing an extra copy of a gene or a fragment thereof into a plant in the “sense orientation” with respect to a promoter for its expression, which as used herein refers to the same orientation as transcription and translation (if it occurs) of the sequence relative to the sequence in the target gene. The size of the sense fragment, its correspondence to target gene regions, and its degree of homology to the target gene are as for the antisense sequences described above. In some instances the additional copy of the gene sequence interferes with the expression of the target plant gene. Reference is made to Patent specification WO 97/20936 and European patent specification 0465572 for methods of implementing co-suppression approaches. The antisense, co-suppression or double stranded RNA molecules may also comprise a largely double-stranded RNA region, preferably comprising a nuclear localization signal, as described in WO 03/076619.

Any of these technologies for reducing gene expression can be used to coordinately reduce the activity of multiple genes. For example, one RNA molecule can be targeted against a family of related genes by targeting a region of the genes which is in common. Alternatively, unrelated genes may be targeted by including multiple regions in one RNA molecule, each region targeting a different gene. This can readily be done by fusing the multiple regions under the control of a single promoter, such as in Example 5.

Methods of Introducing Nucleic Acids into Plant Cells/Transformation

A number of techniques are available for the introduction of nucleic acid molecules into a plant host cell, well known to workers in the art. The term “transformation” means alteration of the genotype of an organism, for example a bacterium or a plant, by the introduction of a foreign or exogenous nucleic acid. By “transformant” is meant an organism so altered. As used herein the term “transgenic” refers to a genetically modified plant in which the endogenous genome is supplemented or modified by the integration, or stable maintenance in a replicable non-integrated form, of an introduced foreign or exogenous gene or sequence. By “transgene” is meant a foreign or exogenous gene or sequence that is introduced into the genome of a plant. The nucleic acid molecule may be stably integrated into the genome of the plant, or it may be replicated as an extrachromosomal element. By “genome” is meant the total inherited genetic complement of the cell, plant or plant part, and includes chromosomal DNA, plastid DNA, mitochondrial DNA and extrachromosomal DNA molecules. The term “regeneration” as used herein in relation to plant materials means growing a whole, differentiated plant from a plant cell, a group of plant cells, a plant part such as, for example, from an embryo, scutellum, protoplast, callus, or other tissue, but not including growth of a plant from a seed.

The particular choice of a transformation technology will be determined by its efficiency to transform certain plant species as well as the experience and preference of the person practicing the invention with a particular methodology of choice. It will be apparent to the skilled person that the particular choice of a transformation system to introduce a nucleic acid construct into plant cells is not essential to or a limitation of the invention, provided it achieves an acceptable level of nucleic acid transfer. Guidance in the practical implementation of transformation systems for plant improvement is provided by Birch, Ann Rev Plant Physiol Plant Mol Biol. 48: 297-326, 1997.

In principle, both dicotyledonous and monocotyledonous plants that are amenable to transformation can be modified by introducing a nucleic acid construct according to the invention into a recipient cell and growing a new plant that harbors and expresses a polynucleotide according to the invention.

Introduction and expression of foreign or exogenous polynucleotides in dicotyledonous plants such as cotton, tobacco, potato and legumes or monocotyledonous plants such as cereals, including wheat, barley, rice, corn, oats, rye and sorghum has been shown to be possible using the T-DNA of the tumor-inducing (Ti) plasmid of Agrobacterium tumefaciens (See, for example, Umbeck, U.S. Pat. No. 5,004,863, and International application PCT/US93/02480). A construct of the invention may be introduced into a plant cell utilizing A. tumefaciens containing the Ti plasmid. In using an A. tumefaciens culture as a transformation vehicle, it is most advantageous to use a non-oncogenic strain of the Agrobacterium as the vector carrier so that normal non-oncogenic differentiation of the transformed tissues is possible. It is preferred that the Agrobacterium harbors a binary Ti plasmid system. Such a binary system comprises (1) a first Ti plasmid having a virulence region essential for the introduction of transfer DNA (T-DNA) into plants, and (2) a chimeric plasmid. The chimeric plasmid contains at least one border region of the T-DNA region of a wild-type Ti plasmid flanking the nucleic acid to be transferred. Binary Ti plasmid systems have been shown effective to transform plant cells as, for example, described by De Framond, Biotechnology, 1: 262, 1983 and Hoekema et al., Nature, 303: 179, 1983. Such a binary system is preferred inter alia because it does not require integration into the Ti plasmid in Agrobacterium.

Methods involving the use of Agrobacterium include, but are not limited to transformation of plant cells or tissues with Agrobacterium such as transformation of seeds, apices or meristems with Agrobacterium, or inoculation in planta such as the floral-dip method as described by Bechtold et al., C.R. Acad. Sci. Paris, 316: 1194, 1993. This approach is based on the infiltration of a suspension of Agrobacterium cells. Alternatively, the chimeric construct may be introduced using root-inducing (Ri) plasmids of Agrobacterium as vectors.

Methods for transformation of cotton plants by introduction of an exogenous nucleic acid and for regeneration of plants from cells by somatic embryogenesis are well known in the art,

Other methods for introducing the nucleic acid construct into a plant cell are by electroporation, or high velocity ballistic penetration by small particles (also known as particle bombardment or microprojectile bombardment) with the nucleic acid to be introduced contained either within the matrix of small beads or particles, or on the surface thereof as, for example described by Klein et al., Nature, 327: 70, 1987.

As used herein, an “induced mutation” is an artificially induced genetic variation which may be the result of chemical, radiation or biologically-based mutagenesis, for example transposon or T-DNA insertion. Preferred mutations are null mutations such as nonsense mutations, frameshift mutations, insertional mutations or splice-site variants which completely inactivate the gene of interest. Nucleotide insertional derivatives include 5′ and 3′ terminal fusions as well as intra-sequence insertions of single or multiple nucleotides. Insertional nucleotide sequence variants are those in which one or more nucleotides are introduced into the nucleotide sequence, which may be obtained by random insertion with suitable screening of the resulting products. Deletional variants are characterised by the removal of one or more nucleotides from the sequence. Preferably, a mutant gene has only a single insertion or deletion of a sequence of nucleotides relative to the wild-type gene. Substitutional nucleotide variants are those in which at least one nucleotide in the sequence has been removed and a different nucleotide inserted in its place. The preferred number of nucleotides affected by substitutions in a mutant gene relative to the wild-type gene is a maximum of ten nucleotides, more preferably a maximum of 9, 8, 7, 6, 5, 4, 3, or 2, or only one nucleotide. Such a substitution may be “silent” in that the substitution does not change the amino acid defined by the codon. Alternatively, conservative substituents are designed to alter one amino acid for another similar acting amino acid.

The term “mutation” as used herein does not include silent nucleotide substitutions which do not affect the activity of the gene, and therefore includes only alterations in the gene sequence which affect the gene activity. The term “polymorphism” refers to any change in the nucleotide sequence including such silent nucleotide substitutions.

Mutagenesis can be achieved by chemical or radiation means, for example EMS or sodium azide (Zwar and Chandler, Planta 197: 39-48, 1995) treatment of seed, or gamma irradiation, well know in the art. Isolation of mutants may be achieved by screening mutagenised plants or seed. In a polyploid plant such as cotton, screening is preferably done in a genotype that is already lacks one of the enzyme activities, so that a mutant entirely lacking the functional activity is sought. Alternatively, the mutation may be identified using techniques such as “tilling” in a population mutagenised with an agent such as EMS (Slade and Knauf, Transgenic Res. 14: 109-115, 2005). Such mutations may then be introduced into desirable genetic backgrounds by crossing the mutant with a plant of the desired genetic background and performing a suitable number of backcrosses to cross out the originally undesired parent background. The invention clearly extends to methods of producing or identifying such plants or the seed produced by such plants.

The process of producing plants of the invention may include mutagenesis and/or screening steps such as TILLING (Targeting Induced Local Lesions IN Genomes). In a first step, introduced mutations such as novel single base pair changes are induced in a population of plants by treating cells, seeds, pollen or other plant parts with a chemical mutagen or radiation, and then advancing plants to a generation where mutations will be stably inherited. DNA is extracted, and seeds are stored from all members of the population to create a resource that can be accessed repeatedly over time. For a TILLING assay, PCR primers are designed to specifically amplify a single gene target of interest. Specificity is especially important if a target is a member of a gene family or part of a polyploid genome. Next, dye-labeled primers can be used to amplify PCR products from pooled DNA of multiple individuals. These PCR products are denatured and reannealed to allow the formation of mismatched base pairs. Mismatches, or heteroduplexes, represent both naturally occurring single nucleotide polymorphisms (SNPs) (i.e., several plants from the population are likely to carry the same polymorphism) and induced SNPs (i.e., only rare individual plants are likely to display the mutation). After heteroduplex formation, the use of an endonuclease, such as Cell, that recognizes and cleaves mismatched DNA is the key to discovering novel SNPs within a TILLING population.

Using this approach, many thousands of plants can be screened to identify any individual with a single base change as well as small insertions or deletions (1-30 bp) in any gene or specific region of the genome. Genomic fragments being assayed can range in size anywhere from 0.3 to 1.6 kb. At 8-fold pooling, 1.4 kb fragments (discounting the ends of fragments where SNP detection is problematic due to noise) and 96 lanes per assay, this combination allows up to a million base pairs of genomic DNA to be screened per single assay, making TILLING a high-throughput technique TILLING is further described in Slade and Knauf, 2005 (supra), and Henikoff et al., Plant Physiol. 135: 630-636, 2004, herein incorporated by reference.

In addition to allowing efficient detection of mutations, high-throughput TILLING technology is ideal for the detection of natural polymorphisms. Therefore, interrogating an unknown homologous DNA by heteroduplexing to a known sequence reveals the number and position of polymorphic sites. Both nucleotide changes and small insertions and deletions are identified, including at least some repeat number polymorphisms. This has been called Ecotilling (Comai et al., Plant J. 37: 778-786, 2004).

As used herein, the term “genetically linked” refers to a marker locus and a second locus being sufficiently close on a chromosome that they will be inherited together in more than 50% of meioses, e.g., not randomly. This definition includes the situation where the marker locus and second locus form part of the same gene. Furthermore, this definition includes the situation where the marker locus comprises a polymorphism that is responsible for the trait of interest (in other words the marker locus is directly “linked” to the phenotype). Thus, the percent of recombination observed between the loci per generation (centimorgans (cM)), will be less than 50. In particular embodiments of the invention, genetically linked loci may be 45, 35, 25, 15, 10, 5, 4, 3, 2, or 1 or less cM apart on a chromosome. Preferably, the markers are less than 5 cM or 2 cM apart and most preferably about 0 cM apart.

As used herein, the “other genetic markers” may be any molecules which are linked to a desired trait of a cotton plant. Such markers are well known to those skilled in the art and include molecular markers linked to genes determining traits such disease resistance, yield, plant morphology, lint quality. Any molecular biological technique known in the art which is capable of detecting alleles of genes of interest can be used in the methods of the present invention. Such methods include, but are not limited to, the use of nucleic acid amplification, nucleic acid sequencing, nucleic acid hybridization with suitably labelled probes, single-strand conformational analysis (SSCA), denaturing gradient gel electrophoresis (DGGE), heteroduplex analysis (HET), chemical cleavage analysis (CCM), catalytic nucleic acid cleavage or a combination thereof. The invention also includes the use of molecular marker techniques to detect polymorphisms linked to alleles of. Such methods include the detection or analysis of restriction fragment length polymorphisms (RFLP), RAPD, amplified fragment length polymorphisms (AFLP) and microsatellite (simple sequence repeat, SSR) polymorphisms. The closely linked markers can be obtained readily by methods well known in the art, such as Bulked Segregant Analysis.

The “polymerase chain reaction” (“PCR”) is a reaction in which replicate copies are made of a target polynucleotide using a “pair of primers” or “set of primers” consisting of “upstream” and a “downstream” primer, and a catalyst of polymerization, such as a DNA polymerase, and typically a thermally-stable polymerase enzyme. Methods for PCR are known in the art, and are taught, for example, in “PCR” (McPherson and Moller (Ed), BIOS Scientific Publishers Ltd, Oxford, 2000). PCR can be performed on cDNA obtained from reverse transcribing mRNA isolated from plant cells expressing an SSII gene or on genomic DNA isolated from a plant. A primer in this context is an oligonucleotide sequence that is capable of hybridising in a sequence specific fashion to the target sequence and being extended during the PCR. Amplicons or PCR products or PCR fragments or amplification products are extension products that comprise the primer and the newly synthesized copies of the target sequences. Primers may be perfectly matched to the target sequence or they may contain internal mismatched bases that can result in the introduction of restriction enzyme or catalytic nucleic acid recognition/cleavage sites in specific target sequences. Primers may also contain additional sequences and/or contain modified or labelled nucleotides to facilitate capture or detection of amplicons. Repeated cycles of heat denaturation of the DNA, annealing of primers to their complementary sequences and extension of the annealed primers with polymerase result in exponential amplification of the target sequence. The terms target or target sequence or template refer to nucleic acid sequences which are amplified.

Methods for direct sequencing of nucleotide sequences are well known to those skilled in the art and can be found for example in Ausubel et al. (supra) and Sambrook et al., 1989 (supra). Sequencing can be carried out by any suitable method, for example, dideoxy sequencing, chemical sequencing or variations thereof. Direct sequencing has the advantage of determining variation in any base pair of a particular sequence.

Plants

The term “plant” as used herein as a noun refers to whole plants and refers to any member of the Kingdom Plantae, but as used as an adjective refers to any substance which is present in, obtained from, derived from, or related to a plant, such as for example, plant organs (e.g. leaves, stems, roots, flowers), single cells (e.g. pollen), seeds, plant cells and the like. Plantlets and germinated seeds from which roots and shoots have emerged are also included within the meaning of “plant”. The term “plant parts” as used herein refers to one or more plant tissues or organs which are obtained from a plant and which comprises genomic DNA of the plant. Plant parts include vegetative structures (for example, leaves, stems), roots, floral organs/structures, seed (including embryo, cotyledons, and seed coat), plant tissue (for example, vascular tissue, ground tissue, and the like), cells and progeny of the same. The term “plant cell” as used herein refers to a cell obtained from a plant or in a plant and includes protoplasts or other cells derived from plants, gamete-producing cells, and cells which regenerate into whole plants. Plant cells may be cells in culture. By “plant tissue” is meant differentiated tissue in a plant or obtained from a plant (“explant”) or undifferentiated tissue derived from immature or mature embryos, seeds, roots, shoots, fruits, tubers, pollen, tumor tissue, such as crown galls, and various forms of aggregations of plant cells in culture, such as calli. Exemplary plant tissues in or from seeds are cotyledon, embryo and embryo axis. The invention accordingly includes plants and plant parts and products comprising these, particularly seed comprising modified oil composition.

As used herein, the term “seed” refers to “mature seed” of a plant, which is either ready for harvesting or has been harvested from the plant, such as is typically harvested commercially in the field, or as “developing seed” which occurs in a plant after fertilisation and prior to seed dormancy being established and before harvest.

A “transgenic plant” as used herein refers to a plant that contains a gene construct not found in a wild-type plant of the same species, variety or cultivar. That is, transgenic plants (transformed plants) contain genetic material (a transgene) that they did not contain prior to the transformation. The transgene may include genetic sequences obtained from or derived from a plant cell, or another plant cell, or a non-plant source, or a synthetic sequence. Typically, the transgene has been introduced into the plant by human manipulation such as, for example, by transformation but any method can be used as one of skill in the art recognizes. The genetic material is preferably stably integrated into the genuine of the plant. The introduced genetic material may comprise sequences that naturally occur in the same species but in a rearranged order or in a different arrangement of elements, for example an antisense sequence. Plants containing such sequences are included herein in “transgenic plants”. A “non-transgenic plant” is one which has not been genetically modified by the introduction of genetic material by recombinant DNA techniques. In a preferred embodiment, the transgenic plants are homozygous for each and every gene that has been introduced (transgene) so that their progeny do not segregate for the desired phenotype.

As used herein, the term “corresponding non-transgenic plant” refers to a plant which is isogenic relative to the transgenic plant but without the transgene of interest. Preferably, the corresponding non-transgenic plant is of the same cultivar or variety as the progenitor of the transgenic plant of interest, or a sibling plant line which lacks the construct, often termed a “segregant”, or a plant of the same cultivar or variety transformed with an “empty vector” construct, and may be a non-transgenic plant. “Wild type”, as used herein, refers to a cell, tissue or plant that has not been modified according to the invention. Wild-type cells, tissue or plants may be used as controls to compare levels of expression of an exogenous nucleic acid or the extent and nature of trait modification with cells, tissue or plants modified as described herein. A typical wild-type plant with respect to cotton is of the variety “Coker”.

Transgenic plants, as defined in the context of the present invention include progeny of the plants which have been genetically modified using recombinant techniques, wherein the progeny comprise the transgene of interest. Such progeny may be obtained by self-fertilisation of the primary transgenic plant or by crossing such plants with another plant of the same species. This would generally be to modulate the production of at least one protein/enzyme defined herein in the desired plant or plant organ. Transgenic plant parts include all parts and cells of said plants comprising the transgene such as, for example, cultured tissues, callus and protoplasts.

Any of several methods may be employed to determine the presence of a transgene in a transformed plant. For example, polymerase chain reaction (PCR) may be used to amplify sequences that are unique to the transformed plant, with detection of the amplified products by gel electrophoresis or other methods. DNA may be extracted from the plants using conventional methods and the PCR reaction carried out using primers to amplify a specific DNA, the presence of which will distinguish the transformed and non-transformed plants. For example, primers may be designed that will amplify a region of DNA from the transformation vector reading into the construct and the reverse primer designed from the gene of interest. These primers will only amplify a fragment if the plant has been successfully transformed. An alternative method to confirm a positive transformant is by Southern blot hybridization, well known in the art. Plants which are transformed may also be identified i.e. distinguished from non-transformed or wild-type plants by their phenotype, for example conferred by the presence of a selectable marker gene, or conferred by the phenotype of modified oil composition of seed of the plant, or related phenotype such as altered enzyme activity.

As used herein, “germination” refers to the emergence of the root tip from the seed coat after imbibition. “Germination rate” refers to the percentage of seeds in a population which have germinated over a period of time, for example 14 or 21 days, after imbibition. A population of seeds can be assessed daily over several days to determine the germination percentage over time. With regard to seeds of the present invention, as used herein the term “germination rate which is substantially the same” means that the germination rate of the transgenic seeds is at least 80% that of isogenic wild-type seeds.

Plants provided by or contemplated for use in the practice of the present invention include angiosperms, including both monocotyledons and dicotyledons. In preferred embodiments, the plants of the present invention are crop plants (for example, cereals and pulses, maize, wheat, potatoes, tapioca, rice, sorghum, millet, cassava, barley, or pea), or other legumes. The plants may be grown for production of edible roots, tubers, leaves, stems, flowers or fruit. Preferably, the plant is a cotton plant. Examples of cereal plants include, but are not limited to, wheat, barley, rice, maize (corn), sorghum, oats, and rye. In an embodiment, the cotton plant is a progeny plant of the line DCS9 (Example 7) and contains the same transgene located in the same position in the genome.

Reference to a “cotton plant” refers to any plant belonging to the genus Gossypium and to any wild relatives, progenitor species, germplasm, cultivar or variety thereof. For example, cotton plants include species such as: G. anapoides, G. anomalum, G. arboreum, G. areysianum, G. aridum, G. armourianum, G. australe, G. barbadense, G. barbosanum, G. henadirense, G. bickii, G. briccetti, G. capitis-viridis, G. costulatum, G. cunningharnii, G. darwinii, G. davidsonii, G. enthyle, G. exiguum, G. gossypioides, G. harknessii, G. herbaceum, G. hirsutum, G. incanum, G. klotzschianum, G. laxum, G. lobatum, G. londonderriense, G. longicalyx, G. marchantii, G. mustelinum, G. nandewarense, G. nelsonii, G. nobile, G. pilosum, G. populifoliurn, G. pulchellum, G. raimondii, G. robinsonii, G. rotundifoliurn, G. schwendimantii, G. somalense, G. soudanense, G. stocksii, G. sturtianum, G. thurberi, G. timorense, G. tomentosum, G. trilobum, G. triphyllum, and G. vindis. Particular species are Gossypium hirsutum (gh) and Gossypium barbadense (gb). As will be appreciated by those of skill in the art, one convenient variety, cultivar or mutant maybe genetically modified and the phenotype bred into related varieties or species by standard breeding techniques. Reference to “progenitor” refers to any of the species, varieties, cultivars, or germplasm, from which a plant is derived. As will be known to those skilled in the art, most commercially useful cotton is a naturally-occurring allotetraploid derived by sexual hybridisation between ancient diploid progenitor parents. Based upon the teaching provided herein, those skilled in the art can readily perform the inventive method on one or more diploid or allotetraploid cottons and produce sexual hybrids between the transgenic plants produced therefrom.

As used herein, the term “derivative species, germplasm or variety” shall be taken to mean any plant species, germplasm or variety that is produced using a stated cotton species, variety, cultivar, or germplasm, using standard procedures of sexual hybridisation, recombinant DNA technology, tissue culture, mutagenesis, or a combination of any one or more said procedures. In particular, interspecific hybrids have been produced between various important cotton species such as G. barbadense, and G. hirsutum, and between certain diploid species, and the production of such interspecific hybrids is routine to those skilled in the art.

As used herein, the term “cotton” refers to any species of the Genus Gossypium, preferably of the species Gossypium hirsutum or Gossypium barbadense. In some embodiments, a suitable control or reference plant is a non-transformed substantially isogenic cotton plant treated in the same way as the “test” plant. Cottonseed oil may be distinguished by the presence therein of CPE and/or CPA fatty acids.

Food Production

In another aspect, the invention provides cotton plants and cottonseed, and products obtained therefrom comprising oil from the seed, particularly cottonseed oil, that is useful for food or feed production, the seed having modified seedoil composition compared to corresponding wild-type seed. Preferably the plant from which the seed is obtained has a reduced level of ghFAD2-1, ghFatB-2 and ghCPA-FAS-2 activities in the seed during development. The cottonseed oil of the present invention is useful for food production and in particular for commercial food production. Such food production might include mixing the cottonseed oil as one ingredient with other ingredients in commercial food production. In preferred embodiments which is desirable for use in food production, the cottonseed oil has a modified composition as specified herein.

Oil is readily isolated from cleaned, de-linted and hulled seeds of the invention using standard methods, for example cooking at high temperatures, pressing, milling using screw press (high pressure) and/or procedures for extraction of oil using solvents, steam and/or high pressure. The oil content of cottonseed, or the content of any fatty acid in the oil of cottonseed is conveniently determined as described herein or as well understood in the art. Alternatively or in addition the procedures of Folch et al., J. Biol. Chem. 226: 497, 1957 or variations thereof as described elsewhere (see for example Liu et al., 2002 (supra)) may be employed. The fatty acid content and/or composition of cotton seed oil may be conveniently determined using gas liquid chromatography against known standard fatty acids, by comparing the fatty acid methyl ester peaks and retention times of reference standards with the sample being tested, and by standard integration of the peaks obtained. However, the present invention is not to be limited by the method of determining the content and/or composition of cottonseed oil, in particular the means for determining fatty acid or other lipid components. Oil is composed almost entirely of triacylglycerols (TAGs) that comprise three fatty acids esterified to a glycerol backbone. To assess the TAG content of oil, oil may be purified such as by solid phase extraction (SPE) on silica gel cartridges. The TAG composition may be qualitatively assessed by reverse phase high resolution liquid chromatography (HPLC) using a refractive index detector and propionitrile as mobile phase. From purified oil, fatty acid methyl esters (FAMEs) are prepared such as by methylation with cold solution of KOH in methanol and the esters analysed by capillary gas chromatography (GC) using high polar columns. From the fatty acid composition, the theoretical TAG composition may be calculated by a computer program employing a typical distribution of fatty acids in the triacylglycerol for cottonseed oil. Mathematical algorithms may be calculated from theoretical and experimental (HPLC) triacylglycerol compositions, and the resulting values compared with those contained in a data base comprising data sets determined by conducting the analysis on different standards of oils.

Food Products

The invention also encompasses foods, beverages or pharmaceutical preparations produced with products comprising the cottonseed oil. The plant of the invention or products derived therefrom containing oil or lint may be used in a variety of applications for human use or consumption. As used herein, “humans” refers to Homo sapiens. The cottonseed oil can be used readily in food processing procedures, in particular frying of food products. The oil may be incorporated into products such as margarine, shortening, salad dressing, mayonnaise, dairy products such as ice cream, yogurt or cheese, or added as an ingredient to other foods or food materials, such as bread, cake, biscuits, pastries, breakfast cereals, pasta, noodles or sauces.

Other parts of the plants of the invention that are edible may be used as foods for human consumption or as feed for animal use. For example, leaves, stems, roots, tubers, fruit, pods or extracts or parts of these comprising cells of the invention from any of these may be used for human or animal consumption. Modified oil content and composition of the plants of the invention and parts thereof may provide advantages for use of these materials as animal feed such as, for example, as feed for pigs, cattle, horses, poultry such as chickens and other animals.

The food or beverage or pharmaceutical preparation may be packaged ready for sale or in bulk form. The invention also provides methods of preparing the food, beverage or pharmaceutical preparation of the invention, and recipes or instructions for preparing such foods or beverages. The methods may comprise the steps of crushing, extracting, milling, cooking, frying, canning, packaging or other processing steps known in the art. The methods or recipes or instructions may include the steps of processing the oil of the invention and/or admixing it with other food ingredients, such as heating or baking the mixture or the product to, for example, at least 100° C. The method may include the step of packaging the product so that it is ready for sale.

Methods

The products of the present invention can be formulated in pharmaceutic compositions which are prepared according to conventional pharmaceutical compounding techniques. See, for example, Remington's Pharmaceutical Sciences, 18^(th) Ed. (1990, Mack Publishing, Company, Easton, Pa., U.S.A.). The composition may contain the active agent or pharmaceutically acceptable derivative active agent. These compositions may comprise, in addition to one of the active substances, a pharmaceutically acceptable excipient, carrier, buffer, stabilizer or other materials well known in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The carrier may take a wide variety of forms depending on the form of preparation desired for administration.

For oral administration, the compounds can be formulated into liquid preparations such as capsules. In preparing the compositions in oral dosage form, any of the usual pharmaceutical media may be employed, such as, for example, water, glycols, oils, alcohols, flavoring agents, preservatives, coloring agents, suspending agents, and the like in the case of oral liquid preparations (such as, for example, suspensions, elixirs and solutions); or carriers such as starches, sugars, diluents, granulating agents, lubricants, binders.

The active agent is preferably administered in a therapeutically effective amount. The actual amount administered and the rate and time-course of administration will depend on the nature and severity of the condition being treated. Prescription of treatment, e.g. decisions on dosage, timing, etc. is within the responsibility of general practitioners or specialists and typically takes account of the disorder to be treated, the condition of the individual patient, the site of delivery, the method of administration and other factors known to practitioners. Examples of techniques and protocols can be found in Remington's Pharmaceutical Sciences, (supra).

Industrial Use

The plant products, preferably oil, may be used in production of industrial products such as, for example, ethanol.

The present invention is further described by the following non-limiting Examples.

Example 1 Illustrative Methods and Materials Isolation of RNA

Two grams of cotton embryos or leaf tissue frozen with liquid nitrogen were ground to a fine powder using a mortar and pestle and transferred to a beaker containing 22 mls cold extraction buffer and stirred constantly. The extraction buffer contained 200 mM Tris-HCl pH8.5, 1.5% Lithium dodecylsulfate, 300 mM LiCl, 10 mM NS₂EDTA, 1% sodium deoxycholate, Nonidet P-40. This was followed by adding 5% insoluble PVP, 90 mM mercaptoethanol, 10 mM DTT (dithiothreitol), 0.1% DEPC and stirred for 10 min prior to being transferred to a Corex tube. Then 18.4 ml of 3M ammonium acetate was added and mixed well. It was centrifuged at 6,000× rpm for 20 min at 4° C. The supernatant was transferred to a new tube and precipitated by adding 1/10 volume of 3 M NaAc, pH5.2 and ½ final volume of cold isopropanol and stored at −20° C. for 1 hour prior to centrifugation at 6,000× rpm for 30 min using a swing rotor. The pellet was resuspended in 1 ml dH₂O and transferred to two Eppendorf tubes (500 μl in each tube). The suspension was extracted with an equal volume of phenol/chloroform/isoamyl alcohol solution (25:24:1) and the phases were separated by centrifugation for 5 min at 4° C. The aqueous top layer was carefully transferred into a new Eppendorf tube and it was extracted again with chloroform as above. Half volume of 5M LiCl was added to the aqueous sample, mixed well and left on ice for 3 hours prior to centrifugation at 12,000× rpm for 15 min at 4° C. The pellet was resuspended in 50 μl dH₂O. Finally, the RNA sample was precipitated by adding 5 μl NaAc and 138 μl cold ethanol and incubated on dry ice for 30 minute prior to centrifugation for 15 min at 4° C. The RNA pellet was dried under vacuum and then dissolved in 30 μl RNase-free H₂O.

Construction of a Cottonseed cDNA Library

Cotton poly(A)⁺ RNA was isolated from total RNA prepared as described above, using a mRNA purification kit (Pharmacia), essentially as described by the manufacturer. To prepare cDNA, a cDNA synthesis kit (Pharmacia) was used, essentially as described by the manufacturer, using 1-5 μg poly(A)⁺ RNA as starting material. The double-stranded cDNA product was blunt-ended, and ligated to EcoRI/NotI adaptors, using standard procedures. Following the removal of excess unligated adaptors, the cDNA was cloned into the bacteriophage vector Lambda ZAPII (Stratagene, USA), and packaged using a commercially-available packaging system (Stratagene, USA), according to the manufacturer's instructions.

The cDNA libraries described herein generally contained about 92% recombinant bacteriophage particles, in a total of about 1.5×10⁷ plaque forming units (pfu) per ml of unamplified library.

Following plaque-purification of positively hybridizing plaques, the ExAssist/SOLR system (Stratagene, USA) was used to excise the pBluescript SK(−) phagemid from the Lambda ZAPII vector, as described by the manufacturer.

All other methods such as gel electrophoresis, transfer of nucleic acids to membranes for hybridisation, preparation of labelled DNA probes, and screening of cDNA libraries were by standard methods (Ausubel et al., (supra)). Unless otherwise stated hybridization conditions were as described by Khandjian, Bio/Technology, 5: 165-167, 1987, herein incorporated by reference) using 50 mM Tris-HCl pH7.5, 1M NaCl, 50% formamide, 10×Denhardt's solution, 10% dextran sulfate, 1% SDS, 0.1% sodium pyrophosphate, 0.1 mg/ml herring sperm DNA at 42° C. Membranes were then briefly washed in 2×SSC, 0.1% SDS at 65° C., followed by two further washes in 0.2×SSC, 0.1% SDS at 65° C. for 15 min each (high stringency).

Example 2 Isolation of FAD2 Genes from Cotton

Four different FAD2 genes have been isolated from cotton, each encoding possible microsomal oleoyl-Δ12 desaturases which could desaturate oleic acid to linoleic acid (Liu et al., 1999a (supra), Liu et al., 1999b (supra); Kargiotidou et al., Journal of Experimental Botany 2008 59(8): 2043-2056, 2008, both herein incorporated by reference). A first gene, designated ghFAD2-1, was specifically expressed in developing seeds at about the same time as active oil biosynthesis (Liu et al., 1999a (supra)). Two nucleotide sequences for ghFAD2-1 are presented herein (SEQ ID Nos: 1 and 24) which are 96% identical along their full lengths and therefore probably represent cDNAs corresponding to either different alleles or more likely the homoeologous FAD2-1 genes in the tetraploid cotton. A second gene, ghFAD2-2, (Accession No. Y10112) had a low level constitutive expression and was expressed at a low level throughout seed development (Pirtle et al., 2001 (supra)). The nucleotide sequence of ghFAD2-2 (SEQ ID NO: 26) is about 72% identical to the central half of ghFAD2-1 (SEQ ID NO: 1). The third and fourth members ghFAD2-3 (Accession No. AF331163) and ghFAD2-4 (Accession No. AY279314) appeared to be expressed more highly in leaves and other cotton tissues rather than seeds (Kargiotidou et al., 2008 (supra)). ghFAD2-3 and ghFAD2-4 have nucleotide sequences which are about 72% identical to ghFAD2-1 (SEQ ID NO: 1).

Based on these observations and the previous production of high-oleic cottonseed oil by RNAi down-regulation of ghFAD2-1 (Liu et al., Plant Physiol. 129: 1732-1743, 2002; U.S. Pat. No. 6,974,898), this gene was thought to encode the major FAD2 activity in cotton seeds. Therefore, a region of the ghFAD2-1 gene having the sequence of nucleotides 5-354 of SEQ ID NO: 1) was selected to make an RNAi construct for down-regulation of the gene. This was the same region as described by Liu et al., 2002 (supra) and was expected to be specific for ghFAD2-1. Other regions of the gene could equally have been selected. For example, U.S. Pat. No. 6,974,898 used a 92 bp region from the 5′-UTR of ghFAD2-1, and Liu et al., 2002 (supra)), used a 540 bp region from the 5′ end of the transcribed part of the gene. The nucleotide and amino acid sequence of FAD-2-1 is shown in FIG. 3.

Example 3 Isolation of FatB Genes from Cotton

Two cDNA clones encoding proteins with homology to FatB in cotton were identified and isolated from a developing cottonseed cDNA library (Example 1) as follows. A PCR fragment corresponding to approximately 480 bp of the first exon of the ghFatB-1 gene (Yoder et al., 1999 (supra); accession number: AF076535) corresponding in sequence to nucleotides 210 to 713 of SEQ ID NO: 3 was amplified using forward (sense) and reverse (antisense) primers: 5′-atggttgctactgctgtgac-3′ (SEQ ID NO: 29 and 5′-ctgtaaatgattcattagtgt-3′ (SEQ ID NO: 30) and template RNA obtained from developing cotton embryos (Example 1). The PCR fragment was used to probe the cDNA library under high stringency and two different FatB-like cDNAs were isolated. These were designated ghFatB-2 and ghFatB-3. Both sequences appeared to be full length cDNAs as they had untranslated regions at both 5′ and 3′ ends. The ghFatB-2 cDNA was 1647 bp long (SEQ ID NO: 5) and encoded a predicted protein of 421 amino acids (SEQ ID NO: 6), which included the signal sequence used for translocation of the protein into the plastid. The ghFatB-3 cDNA was 1498 bp long (SEQ ID NO: 7) and encoded a predicted protein of 419 amino acids (SEQ ID NO: 8).

The predicted amino acid sequences of ghFatB-2, and -3 each had 60-75% identity along their full length with several reported FatB thioesterases, such as those from Arabidopsis and soybean (Accession No. DQ418764) and Brassica juncea (DQ856315), whereas only 30-40% homology with FatA thioesterase from dicot plants, such as Arabidopsis (AK176105). The putative polypeptides encoded by the coding region of ghFatB-2 and -3 showed 89% identity to each other. Because their 3′UTR sequences were quite different, it was thought that they were derived from two different genes belonging to a FatB gene family in cotton. A cDNA encoding FatB and its corresponding structural gene were isolated by Pirtle et al., Plant Cell Physiology, 40: 155-163, 1999, herein incorporated by reference (cDNA: Accession No. AF034266; structural gene: AF076535). Compared to the previously isolated ghFatB-1 (Yoder et al., 1999 (supra); accession number: AF076535), ghFatB-2 has about 87% identity and ghFatB-3 has about 84% identity. As do all the acyl-ACP thioesterases characterised to date, the cotton FatB thioesterases have transit peptide sequences in the N-terminus to direct the proteins into plastids. The exact transit peptide cleavage site is not known, but has been suggested to be somewhere at the beginning of a highly conserved hydrophobic region unique to the plant FatB sequences (Jones et al., 1995 (supra)). FIGS. 4 and 5 show the nucleotide sequences and putative polypeptides of ghFatB-2 and -3, respectively.

It has previously been suggested that plant FatB genes are constitutively expressed (Dorman et al., Arch. Biochem. Biophys. 316: 612-618, 1995). Consistent with this, expression analysis showed that the ghFatB-1 gene was expressed in embryos, seedlings and leaves of mature cotton plants (Pirtle et al, 1999 (supra)). Both ghFatB-2 and -3 were thought to be expressed in developing seeds as they were isolated from the cottonseed cDNA library as described above, and possibly other tissues. The expression level of ghFatB-2 in seeds was higher than ghFatB-3, and therefore the former was suggested to encode the major FatB activity in cotton seed. However, to establish that this gene rather than the other two encoded the major FatB activity in cottonseed, it was necessary to show that its inactivation would result in reduced thioesterase activity and reduced release of palmitic acid from the plastid. It was also possible that two or three of the genes in combination would need to be silenced to reduce palmitic acid levels. Therefore, a gene silencing construct was made using a region from ghFatB-2, having the sequence of nucleotides 458-843 of SEQ ID NO: 5.

Example 4 Cloning of Genes Encoding Cyclopropane Fatty Acid Synthase (CPA-FAS) in Cotton

CPA-FAS catalyses the first committed step in production of cyclopropane fatty acids, the conversion of oleic acid to DHS. Two EST sequences from G. hirsutum were identified as being differentially expressed after infection of cotton roots and hypocotyls with Fusarium oxysporeum (Dowd et al., 2004 (supra)). One of the EST sequences, CD486555, was used as a DNA probe to screen the cDNA library made from developing cottonseed (Example 1) and a second cDNA library made from RNA obtained from cotton roots. The DNA sequence of the probe DNA is shown in FIG. 6 (SEQ ID NO: 9).

After high stringency hybridization with the probe, two different full length cDNAs with unique 5′ and 3′ UTR sequences were isolated from the cDNA library made from cotton root RNA. A third cDNA clone was isolated from the cottonseed cDNA library. They were designated as ghCPA-FAS-1, 2 and -3 respectively. The DNA sequences and the predicted amino acid sequences of the encoded polypeptides are shown in FIGS. 7-9 (SEQ ID NO: 10-15).

The deduced ghCPA-FAS polypeptides each comprised 865-873 amino acids and had calculated molecular masses of approximately 99 kDa. This probably represented the mature protein since CPA-FAS enzyme, being active in the ER, was not expected to have a 5′ signal peptide. Similarly to CPA-FAS from Sterculia foetida and the homologous proteins from Arabidopsis (Accession No. AT23510) and rice (AK069115) predicted from genomic sequences, the encoded ghCPA-FAS proteins had an N-terminal FAD-binding domain fused to a C-terminal domain which had homology to various methyltransferases. This was consistent with predicted CPA-FAS activity of the proteins. At the N-terminus, the first 20 amino acids of the ghCPA-FAS proteins appeared to be hydrophobic and were thought to be involved in membrane anchoring.

When the deduced amino acid sequences of the three different ghCPA-FAS cDNAs were compared with homolgous DNA sequences from Sterculia foetida, Arabidopsis and rice, it was observed that ghCPA-FAS-1 (AY574036) and ghCPA-FAS-2 (AY574037) shared 97% amino acid identity, but only 64-65% identity to ghCPA-FAS-3 (AY574038). In contrast, ghCPA-FAS-3 showed higher sequence homology with each of the Arabidopsis genes −74% amino acid identity with At23510, and 75% amino acid identity with At23530. This suggested that ghCPA-FAS-3 evolved separately before cotton speciation. Arabidopsis and rice are not known to accumulate CPA or CPE fatty acids and therefore the functionality of the CPA-FAS genes in these plants is determined.

The genomic organization of CPA-FAS genes in cotton was investigated by Southern blot hybridization analysis using the protein coding region of ghCPA-FAS-1 as a probe. At least three hybridizing bands were detected in HindIII digested DNA from diploid cottons, while there were twice as many hybridizing bands in tetraploid cottons (FIG. 10). It was concluded that each of the three ghCPA-FAS genes were represented by a single locus in diploid Gossypium and two homoeologous loci in tetraploid cottons. This demonstrated that allotetraploid cotton contained two copies of each of the three genes present in the A- and D-genome diploid progenitors.

Expression of the cotton CPA-FAS genes were analysed, looking for differentially expression in cotton tissues. As shown in FIG. 11, the analysis of total RNA extracted from various cotton tissues including roots, hypocotyls, leaves and developing embryos at various times after anthesis revealed that the ghCPA-FAS-1 transcript level was high in roots and hypocotyls, but not detected in leaves and developing embryos, while ghCPA-FAS-2 expression was detected in all tissues examined except the leaves. In the developing embryos, maximal transcript levels of ghCPA-FAS-2 were found in embryos during the middle part of seed development, from approximately 20-40 days after anthesis. This was the main time period for oil production in developing cotton embryos. It was therefore predicted that ghCPA-FAS-2 played a key role in determining the biosynthesis of cyclopropenoid fatty acids in cottonseed and therefore was a candidate target gene for down-regulation to reduce CPA and CPE fatty acids in cottonseed oil.

Example 5 Genetic Construct to Simultaneously Down-Regulate ghFAD2-1, ghCPA-FAS-2 and ghFatB-2 in Cottonseed

A genetic construct to express a chimeric hairpin RNA molecule for RNAi mediated reduction of gene expression was made as follows. The RNAi gene silencing construct was designed to simultaneously target three different genes with the goal of achieving significant reductions in palmitic acid and cyclopropane fatty acids in combination with significantly increased oleic acid in cottonseed oil. The construct is shown schematically in FIG. 12 and contained an inverted repeat of a chimeric sequence made from 350 bp of ghFAD2-1, 442 bp of ghCPA-FAS-2 and 358 bp of ghFatB-1 fused together. The inverted repeat units of this chimeric sequence were separated by Intron 1 from the ghFad2-1 gene, which was 1120 bp long, with intact 5′ and 3′ exon/intron boundaries (FIG. 13, fragment C). The intron acted as a spacer to stabilize the inverted repeat and thereby facilitate the cloning of the inverted repeat in the plasmid vector in E. coli. To achieve seed specific expression, the inverted repeat sequence was placed under the control of a soybean lectin promoter (Lec-P) and a transcription terminator/polyadenylation sequence (Lec-T) (Cho et al., Plant Molecular Biology Reporter 13: 255-269, 1995). The hairpin RNA-expressing gene was positioned adjacent to the 3′ end of a selectable marker gene comprised of an NPTII protein coding region driven by the sub-clover stunt virus promoter (Sc1-P) and terminator (Sc3-T). The specific sequences used are shown in FIG. 13 (SEQ ID NOs: 16-23). This genetic construct was named the MonoCott construct.

A second genetic construct, designated LY-2, was also made. This was the same as the MonoCott construct except that the 442 bp segments of the ghCPA-FAS-2 gene were replaced with a region of a cotton gene encoding cadinene hydroxylase, an enzyme requited for synthesis of gossypol in developing seeds. To make LY-2, a 401 bp DNA fragment derived from the gene ghCAD-H encoding (+)-delta-cadinene-8-hydroxylase (accession number: AF332974), corresponding to nucleotides having the sequence 1420 to 1821 of SEQ ID NO: 28 were amplified in PCR reactions using the primers: S1: 5′-cctgagaggttcttgactgatcatg-3′ (SEQ ID NO: 31) and A1: 5′-gcttatgatgtataataaacacattat-3′ (SEQ ID NO: 32). This fragment was substituted for the ghCPA-FAS-2 portions in the MonoCott construct to make LY-2.

Example 6 Transformation of Cotton with the Monocott construct

The MonoCott and LY-2 genetic constructs were each inserted into a binary vector and introduced into Agrobacterium tumefaciens strain AGL1. The transformed bacteria were used to transform cotton variety Coker315 as described by Liu et al., 2002 (supra). Briefly, cotyledons excised from 10-days old aseptically-grown cotton seedlings were used as explants and were infected and co-cultivated with the A. tumefaciens transformants for a period of two days. This was followed by a six-week period of selection on MS medium (Murashige and Skoog, Physiologia Plantarum. 15: 473-497, 1962) containing 0.1 mg/l 2,4-D, 0.1 mg/l kinetin, 50 mg/l kanamycin sulphate, and 25 mg/l cefotaxime. Healthy calli derived from the cotyledon explants were then transferred to MS medium containing 5 mg/l 6-(γ,γ-dimethylallylamino)-purine (2ip), 0.1 mg/l naphthalene acetic acid (NAA), 25 mg/1 kanamycin, and 250 mg/l cefotaxime for a second period of six weeks at 28° C. Somatic embryos started to form after about six to ten weeks of incubation and were transferred to fresh plates, but without added phytohormone or antibiotics, until they germinated. Plantlets that developed from the somatic embryos were subsequently transferred to soil and maintained in a glasshouse once leaves and roots were developed, with 28/20° C. (day/night) growth temperature.

Six independent cotton lines transformed with the MonoCott RNAi construct were regenerated from calli and allowed to grow to maturity in the greenhouse, flowering and producing seed as normal. No obvious phenotypic differences were observed between the transgenic plants and the non-transgenic (wild-type) parental plants of the variety Coker315. Ten independent cotton lines transformed with the LY-2 RNAi construct were also regenerated from calli and treated similarly.

Example 7 Phenotypic Analysis of Cotton Transformants

A portion consisting of about ⅛ of the cotyledons of the mature seeds was excised from the T₂ seeds obtained from the primary T₁ transgenic plants and each portion subjected to of fatty acid composition analysis by FAME and GC-MS. Total lipids were isolated using the method of Bligh et al., Canadian Journal of Biochemistry and Physiology 37: 911-917, 1959 and fatty acid methylesters (FAMEs) were prepared using standard methods as described by Liu et al., 2002 (supra). FAMEs were subsequently separated by gas chromatography (GC), using an Agilent 6890 GC fitted with a forte GC capillary column (30 m×0.25 mm). Fatty acids were identified by reference to FAME standards.

Seeds of transgenic line DCS9-34 had a fatty acid composition having a markedly increased level of oleic acid, in combination with reduced palmitic acid and reduced cyclopropane fatty acid levels. This transgenic line was selected and bred to homozygosity. Data showing the inheritance of fatty acid composition in seed oil of progeny is given in Table 1. As shown in Table 1, the oleic acid content in the seedoil of line DCS9-34 was increased to about 75%-80% and the palmitic acid content was reduced down to below 10%. In the high-oleic lines previously developed (Liu et al., 2002 (supra)), palmitic acid levels were reduced to 16% of the total fatty acids in the seedoil as a pleiotropic effect of RNAi-mediated down-regulation of ghFAD2-1 (Liu et al., 2002 (supra)). The further reduction of palmitic acid down to 7% obtained with the MonoCott construct was presumed to be due to the combined effect of down-regulation of both ghFAD2-1 and ghFatB-2. Similar phenotypes were seen in the other plants transformed with the MonoCott construct, but to a lesser extent.

In the T₂ seeds obtained from the primary, transgenic DCS9-34 plants, three out of ten seeds were null segregants. Therefore it appeared that the transgene segregated as a single dominant gene with Mendelian inheritance pattern. In the subsequent T₃ seeds, three out of 15 seeds were nulls/segregants lacking the transgene. No null seeds were found in thirty T₄ seeds analysed; therefore these represented a homozygous population. Since only an approximately ⅛ portion of the cotyledons of the T₂ and T₃ seeds were used in the fatty acid analysis, cyclic fatty acids were not detected due to their predominant presence in seed radicals. As also shown in FIG. 14, the fatty acid composition across each of the three generations was characterized by increased oleic acid and reduced palmitic acid levels. These levels remained constant and were stably inherited in plants that were either heterozygous or homozygous for the transgene as shown in Table 2. This correlation clearly demonstrated that stable inheritance of the genetic alteration of fatty acid composition was achieved by transgenic expression of the MonoCott RNAi construct simultaneously targeting the three genes ghFAD2-1, ghCPA-FAS-2 and ghFatB-2.

In the LY-2 transgenic seed, oleic acid levels were also elevated, to above 80% and in some seed greater than 85%. The palmitic acid level in many seeds was about 7%, and the linoleic acid level about 6-10% (Table 2). These altered levels were stably inherited as a Mendelian locus together with the transgene (Table 2).

The cyclopropane fatty acids, including DHS, STC and MVL are not present at significant levels in cotton cotyledons in mature cottonseed, but rather are concentrated in the embryo axes of the mature seeds. In order to analyse cyclopropane fatty acid levels in the transgenic lines, embryo axis were excised and subjected to fatty acid composition analysis. Full fatty acid profile of the DCS9-34 embryo axes, together with the untransformed control, Coker315 and a transgenic line transformed with the LY-2 construct is tabulated in Table 3 and graphed in FIG. 15. LY-2 transformed seed were also analysed. As shown above, LY-2 transformed seed showed similarly modified, low-palmitic and high-oleic levels as DCS9-34-transformed seed. As shown in Table 3, the non-transformed cotton embryo axes, as represented by the untransformed Coker315, contained total cyclopropane fatty acids at a level of 11.5% of total fatty acids (average of 23 randomly sampled seeds). In LY-2 seed, as a result of the substantial increase of oleic acid which is the substrate for CPA-FAS enzyme, each of the three cyclopropane fatty acids DHS. STC and MVL, as well as the total percentage of cyclopropane fatty acids, were increased substantially compared to the untransformed control. This was in sharp contrast to the MonoCott line, DCS9-34, which showed a substantial reduction in all three cyclopropane fatty acids with total cyclic fatty acid level averaging only 3.8% in 26 randomly selected seeds. This represented a reduction of total cyclopropane fatty acids more than 60% compared to wild-type and more than 80% compared to the LY-2 transgenic seed.

Those skilled in the art will appreciate that the invention described herein is susceptible to variations and modifications other than those specifically described. It is to be understood that the invention includes all such variations and modifications. The invention also includes all of the steps, features, compositions and compounds referred to or indicated in this specification, individually or collectively, and any and all combinations of any two or more of said steps or features.

TABLE 1 Seedoil fatty acid composition in the cotton seed of transgenic line DCS9-34, in three generations. Seeds with greater than 20% palmitic acid content were null segregants, and were essentially the same as the wild-type level. % Palm- % % % Lino- Total Gener- Seed itic Stearic Oleic leic % ation No. (16:0) (18:0) (18:1) (18:2) CPFAs T₂  1 24.1 1.8 13.3 58.5 ND  2 22.0 1.8 13.4 60.4 ND  3 11.8 1.6 63.7 21.6 ND  4  9.3 1.6 73.4 14.6 ND  5  9.8 1.7 70.6 16.7 ND  6 22.5 1.8 17.0 56.6 ND  7 11.3 1.6 64.8 20.9 ND  8  9.5 1.8 70.0 17.6 ND  9  8.5 1.6 75.4 13.3 ND 10 10.9 1.6 72.3 14.1 ND T₃  1  8.6 2.2 76.6 12.0 ND  2  9.5 2.2 73.4 14.5 ND  3  8.9 2.6 73.6 14.5 ND  4  7.4 2.4 80.0  9.8 ND  5 22.8 2.4 15.0 58.8 ND  6  7.6 2.3 81.0  8.7 ND  7  9.3 2.4 73.4 14.4 ND  8  8.0 2.5 76.7 12.3 ND  9  8.9 2.6 78.7  9.2 ND 10  9.0 2.6 74.3 13.7 ND 11  7.9 2.9 78.6 10.2 ND 12 23.2 2.8 15.6 57.4 ND 13  9.0 2.6 74.2 13.7 ND 14  7.8 2.2 79.5 10.1 ND 15 23.2 2.7 14.9 58.4 ND T₄  1  8.3 2.3 74.2 12.6 0.2  2  8.2 2.5 75.6 11.2 0.4  3  8.1 2.5 74.9 11.9 0.2  4  8.7 2.3 72.9 13.6 0.2  5  8.0 2.5 75.3 11.6 0.3  6  8.2 2.3 75.2 11.8 0.2  7  7.8 2.6 76.3 10.7 0.3  8  7.6 2.4 76.6 11.0 0.2  9  8.2 2.7 75.1 11.4 0.3 10  8.3 2.5 74.4 12.4 0.2 11  8.0 2.5 75.6 11.5 0.2 12  8.2 2.4 75.5 11.2 0.2 13  7.4 2.5 76.5 11.3 0.2 14  7.8 2.4 76.3 11.3 0.0 15  7.8 2.6 75.2 12.1 0.3 16  8.3 2.2 74.5 12.4 0.3 17  8.2 2.3 74.6 12.3 0.3 18  8.3 2.3 74.1 12.8 0.2 19  8.5 2.3 73.9 12.6 0.3 20  7.8 2.6 75.5 11.7 0.2 21  7.7 2.5 76.3 11.1 0.2 22  8.3 2.6 74.4 12.2 0.3 23  7.9 2.6 73.8 13.2 0.2 24  7.5 2.5 76.7 11.0 0.1 25  8.0 2.5 75.5 11.5 0.2 26  8.2 2.3 74.7 12.0 0.3 27  7.9 2.4 75.6 11.6 0.2 28  7.9 2.6 74.9 12.0 0.3 29  8.1 2.4 75.3 11.8 0.2 30  8.2 2.4 73.8 12.9 0.4 ND: not determined

TABLE 2 Fatty acid composition of three generations of transgenic cotton expressing the LY-2 RNAi construct targeting three genes, namely ghFad2-1, ghCAD-H and ghFatB-2. LY2-1, LY2-8 and LY2-9 appear to show wild-type fatty acid composition and may be non-transformed “escapes”. Sample Myristic Palmitic Stearic Oleic Linoleic Linolenic Arachidic T2 seeds LY2-1 0.88 21.26 1.47 11.34 65.50 0.00 0.00 LY2-2 0.13  8.22 0.87 78.27 12.37 0.21 0.00 LY2-3 0.20  9.65 0.66 74.23 15.21 0.15 0.00 LY2-4 0.00  9.42 1.46 76.76 12.20 0.16 0.00 LY2-5 0.00  8.88 0.60 76.82 13.70 0.00 0.00 LY2-6 0.16  8.10 1.52 80.67  9.36 0.18 0.00 LY2-7 0.22  8.41 1.68 79.97  9.36 0.23 0.14 LY2-8 0.85 21.37 1.73 12.22 63.58 0.24 0.00 LY2-9 0.67 21.45 1.65 11.50 64.45 0.28 0.00 LY2-10 0.21  8.02 1.46 80.51  9.67 0.13 0.00 T3 seeds LY2.2-1 0.35  6.97 2.07 83.35  6.94 0.13 0.19 LY2.2-2 0.43  6.88 2.03 83.10  7.25 0.14 0.17 LY2.2-3 0.34  7.16 1.71 83.37  7.15 0.12 0.16 LY2.2-4 0.12  7.13 2.10 82.05  8.28 0.18 0.14 LY2.2-5 0.14  7.13 1.91 83.54  7.00 0.12 0.17 LY2.2-6 0.11  6.82 2.07 83.79  6.87 0.14 0.19 LY2.2-7 0.12  6.85 1.69 85.53  7.48 0.13 0.20 LY2.2-8 0.15  7.18 2.03 83.11  7.22 0.16 0.16 LY2.2-9 0.12  6.69 1.93 84.04  6.87 0.13 0.23 LY2.2-10 0.32  6.45 1.91 85.02  5.94 0.17 0.19 LY2.2-11 0.24  7.85 1.74 83.46  6.39 0.11 0.18 LY2.2-12 0.22  7.38 1.24 85.48  5.39 0.13 0.17 LY2.2-13 0.35  8.57 1.27 83.34  6.15 0.20 0.12 LY2.2-14 0.19  6.83 1.68 85.62  5.37 0.13 0.19 LY2.2-15 0.23  7.47 1.94 83.22  6.79 0.14 0.21 T4 seeds LY2.2.1-1 0.20  8.96 1.93 77.80 10.41 0.17 0.29 LY2.2.1-2 0.16  7.88 2.15 81.14  8.06 0.18 0.26 LY2.2.1-3 0.17  8.08 2.00 81.33  7.87 0.16 0.26 LY2.2.1-4 0.17  8.96 2.17 78.29  9.61 0.25 0.26 LY2.2.1-5 0.16  8.34 2.39 79.31  8.94 0.21 0.30 LY2.2.1-6 0.17  7.81 2.09 81.32  7.96 0.16 0.30 LY2.2.1-7 0.15  7.77 2.01 81.42  8.00 0.17 0.27 LY2.2.1-8 0.19  8.66 2.03 79.96  8.61 0.15 0.26 LY2.2.1-9 0.18  8.31 2.08 80.60  8.21 0.17 0.27 LY2.2.1-10 0.19  8.77 1.76 80.39  8.28 0.16 0.24 LY2.2.1-11 0.16  8.26 2.03 80.52  8.41 0.18 0.25 LY2.2.1-12 0.26 10.60 2.45 74.43 11.41 0.47 0.30 LY2.2.1-13 0.17  8.02 2.14 81.09  8.01 0.18 0.25 LY2.2.1-14 0.13  7.28 2.24 82.01  7.72 0.18 0.28 LY2.2.1-15 0.17  8.16 1.83 81.27  8.03 0.15 0.26 LY2.2.1-16 0.17  8.04 1.95 81.25  8.03 0.16 0.25 LY2.2.1-17 0.15  7.19 1.83 83.02  7.31 0.14 0.25 LY2.2.1-18 0.20  8.88 2.01 79.40  8.89 0.17 0.27 LY2.2.1-19 0.15  7.70 2.16 81.75  7.69 0.15 0.27 LY2.2.1-20 0.19  8.64 1.89 79.62  9.04 0.16 0.26 LY2.2.1-21 0.18  8.19 2.01 81.25  7.84 0.15 0.25 LY2.2.1-22 0.19  8.56 2.06 80.19  8.35 0.16 0.27 LY2.2.1-23 0.18  8.67 2.03 80.45  8.00 0.20 0.25 LY2.2.1-24 0.16  7.95 1.95 81.53  7.89 0.15 0.26 LY2.2.1-25 0.16  7.92 2.33 81.02  8.02 0.17 0.27 LY2.2.1-26 0.18  8.49 2.08 80.43  8.15 0.17 0.27 LY2.2.1-27 0.18  8.58 2.05 80.19  8.32 0.18 0.27 LY2.2.1-28 0.17  8.26 2.04 80.08  8.88 0.18 0.26 LY2.2.1-29 0.16  7.77 2.04 81.44  7.99 0.17 0.27 LY2.2.1-30 0.18  8.14 1.76 81.16  8.16 0.19 0.24 T4 seeds LY2.2.4-1 0.17  9.14 2.76 79.72  7.65 0.13 0.31 LY2.2.4-2 0.18  9.57 2.82 78.68  8.08 0.17 0.31 LY2.2.4-3 0.15  9.16 3.18 78.75  8.05 0.17 0.31 LY2.2.4-4 0.17  9.28 2.97 79.31  7.62 0.15 0.32 LY2.2.4-5 0.17  9.33 2.56 79.58  7.79 0.15 0.28 LY2.2.4-6 0.17  9.29 2.79 79.09  8.03 0.16 0.29 LY2.2.4-7 0.16  9.42 2.66 78.09  9.00 0.17 0.29 LY2.2.4-8 0.21  9.82 2.59 77.69  9.03 0.18 0.30 LY2.2.4-9 0.19  9.15 2.43 80.02  7.66 0.14 0.28 LY2.2.4-10 0.18  9.00 2.72 79.48  8.10 0.13 0.31 LY2.2.4-11 0.18  9.63 2.99 78.71  7.84 0.17 0.30 LY2.2.4-12 0.22  9.88 2.42 78.79  8.05 0.15 0.31 LY2.2.4-13 0.21  9.62 2.37 79.01  8.22 0.13 0.30 LY2.2.4-14 0.16  9.01 2.92 79.82  7.53 0.15 0.30 LY2.2.4-15 0.18  9.52 2.76 79.06  7.85 0.16 0.29 LY2.2.4-16 0.19  9.75 2.76 78.63  8.05 0.16 0.29 LY2.2.4-17 0.18  9.24 2.38 80.03  7.62 0.14 0.27 LY2.2.4-18 0.20  9.82 2.73 77.41  9.15 0.18 0.31 LY2.2.4-19 0.23 10.18 2.16 78.61  8.36 0.13 0.25 LY2.2.4-20 0.16  9.06 2.74 80.11  7.43 0.14 0.27 LY2.2.4-21 0.17  9.31 2.77 79.66  7.47 0.15 0.31 LY2.2.4-22 0.18  9.26 2.73 79.77  7.44 0.18 0.28 LY2.2.4-23 0.19  8.94 2.38 79.98  7.99 0.13 0.27 LY2.2.4-24 0.19  9.41 2.38 79.71  7.70 0.17 0.27 LY2.2.4-25 0.19  9.47 2.43 79.60  7.74 0.14 0.28 LY2.2.4-26 0.20 10.08 2.84 76.62  9.54 0.17 0.31 LY2.2.4-27 0.21  9.90 2.49 77.69  9.06 0.17 0.29 LY2.2.4-28 0.20  9.84 2.65 78.72  7.91 0.19 0.30 LY2.2.4-29 0.18  9.08 2.90 79.08  8.19 0.14 0.32 LY2.2.4-30 0.16  8.89 2.65 79.82  7.91 0.15 0.27 Reduction of cyclopropane fatty acids in cotton embryo axes of T₄ homozygous DCS9-34 seed

TABLE 3 Fatty acid composition of embryo axes in three types of cottons, including DCS9-34 (MonoCott) with combined traits of HO, LP and low-cyclic fatty acids, LY-2 with HO and LP traits, but increased cyclic fatty acids and Coker315 as the conventional cotton control. DCS9 embryo axes CPFAs 18:1 18:1 Total Seed No 14:0 16:0 16:1 18:0 n-9 n-7 18:2 18:3 DHS MVA STC CPFA  1 0.5 16.6 0.8 2.5 48.5 1.0 25.8 0.8  0.3  2.1 0.5  3.0  2 0.5 15.1 0.8 2.2 47.4 1.0 27.7 0.9  0.4  2.8 0.7  4.0  3 0.6 16.0 0.8 1.5 43.8 1.1 29.3 1.2  0.4  4.1 0.8  5.3  4 0.5 14.7 0.8 2.1 49.0 1.0 26.7 0.8  0.4  2.9 0.7  4.0  5 0.4 13.0 0.8 2.2 54.5 1.0 25.0 0.7  0.2  1.4 0.4  2.1  6 0.6 16.3 0.8 1.5 42.0 1.1 31.5 1.1  0.4  3.4 0.8  4.6  7 0.6 17.3 0.9 1.4 39.5 1.1 32.6 1.1  0.5  3.8 0.9  5.1  8 0.5 14.6 0.8 1.7 47.9 1.0 28.8 0.8  0.2  2.5 0.6  3.4  9 0.5 14.0 0.8 2.3 51.3 1.0 25.5 0.9  0.3  2.4 0.5  3.3 10 0.6 16.0 0.8 1.5 43.7 1.1 30.4 1.0  0.4  3.2 0.7  4.4 11 0.4 14.1 0.7 2.2 49.4 1.0 27.0 0.8  0.3  2.8 0.7  3.8 12 0.4 14.5 0.8 1.7 48.9 1.0 28.3 0.9  0.2  2.2 0.6  3.0 13 0.4 14.8 0.8 2.0 48.5 1.1 27.6 0.7  0.3  2.5 0.7  3.6 14 0.6 16.8 0.9 1.3 40.6 1.1 32.7 1.2  0.3  3.2 0.7  4.2 15 0.6 16.9 0.8 1.5 40.3 1.0 31.2 1.2  0.6  4.3 1.1  5.9 16 0.4 12.4 0.8 2.1 57.5 1.0 23.4 0.6  0.2  0.8 0.3  1.3 17 0.5 15.8 0.8 2.1 43.9 1.0 29.7 0.9  0.5  3.3 0.9  4.7 18 0.6 16.1 0.9 1.4 43.5 1.1 30.7 1.1  0.3  3.1 0.7  4.2 19 0.4 13.1 0.7 2.4 54.6 0.9 23.9 0.8  0.2  2.0 0.5  2.7 20 0.5 15.2 0.9 1.3 45.4 1.2 30.9 1.1  0.2  2.3 0.5  2.9 21 0.6 16.0 0.9 1.4 43.1 1.1 31.1 1.1  0.4  3.2 0.8  4.3 22 0.5 15.2 0.7 1.7 46.8 1.0 28.6 0.9  0.4  2.9 0.7  4.0 23 0.5 14.7 0.9 1.4 46.5 1.2 29.8 1.2  0.2  2.6 0.5  3.3 24 0.5 16.6 0.8 1.7 43.9 1.0 29.1 0.9  0.6  3.5 0.9  5.0 25 0.6 16.8 0.9 1.5 41.0 1.1 31.4 1.2  0.4  3.8 0.9  5.1 26 0.5 15.2 0.8 1.8 47.9 1.1 28.0 1.0  0.2  2.3 0.5  3.0 Average  0.3  2.8 0.7  3.8 LY2 embryo axes 18:1 18:1 Total Seed No 14:0 16:0 16:1 18:0 n-9 n-7 18:2 18:3 DHS MVA STC CPFA  1 0.4 18.1 0.6 5.0 27.5 0.6 20.9 0.8  9.2  9.5 6.3 25.0  2 0.4 18.6 0.5 5.1 22.2 0.5 20.5 1.1 10.3 12.9 6.8 30.0  3 0.4 17.1 0.7 3.6 41.3 0.7 20.0 0.9  4.4  6.2 4.0 14.6  4 0.4 16.8 0.7 4.3 34.2 0.7 19.3 1.1  6.9  8.7 6.0 21.6  5 0.3 14.7 0.6 4.5 42.4 0.6 15.6 0.8  7.1  7.4 5.1 19.6  6 0.3 15.5 0.6 4.3 37.4 0.6 18.4 0.6  7.8  7.8 5.7 21.3  7 0.3 14.3 0.6 4.1 46.1 0.6 17.2 0.7  4.9  5.8 4.5 15.2  8 0.5 18.5 0.6 4.1 29.2 0.7 21.9 1.0  7.0  9.0 6.6 22.6  9 0.3 16.4 0.6 4.5 33.3 0.6 18.6 1.2  7.5  9.5 6.5 23.5 10 0.3 13.4 0.6 4.5 44.9 0.6 15.2 0.7  6.9  7.1 5.0 19.0 11 0.4 15.5 0.6 4.6 42.0 0.6 17.0 0.7  6.9  5.9 5.0 17.7 12 0.4 16.5 0.6 4.9 32.6 0.6 18.7 1.1  8.4  9.2 5.9 23.5 13 0.4 16.1 0.7 3.9 33.0 0.7 20.3 1.0  7.3  9.3 6.4 23.1 14 0.4 16.1 0.6 4.5 43.0 0.6 17.2 0.7  5.6  6.2 4.1 15.9 15 0.4 16.7 0.6 4.2 38.9 0.6 19.0 0.8  5.7  7.1 5.0 17.8 16 0.4 18.1 0.5 4.7 37.4 0.6 18.7 0.8  6.5  6.6 4.6 17.6 17 0.3 14.3 0.6 4.4 46.0 0.6 15.2 0.6  6.7  6.3 4.2 17.1 18 0.3 16.2 0.6 5.1 35.7 0.6 18.0 0.8  8.6  7.2 5.8 21.6 19 0.3 14.0 0.6 4.2 44.6 0.6 15.5 0.7  6.4  7.2 5.1 18.7 20 0.7 21.7 0.6 4.2 19.9 0.6 26.1 1.2  7.0 11.4 5.6 24.1 21 0.3 13.7 0.6 4.3 47.3 0.6 15.4 0.7  5.5  6.3 4.4 16.1 22 0.3 13.5 0.6 3.8 49.0 0.6 16.3 0.6  5.1  5.2 4.2 14.4 23 0.3 14.2 0.6 4.1 45.5 0.6 16.4 0.7  5.8  6.5 4.4 16.7 24 0.3 15.8 0.7 4.3 37.1 0.6 18.5 0.8  7.4  7.0 6.6 20.9 25 0.5 19.5 0.6 4.5 25.5 0.6 21.8 1.2  7.9 10.6 6.4 24.9 Average  6.9  7.8 5.4 20.1 Coker embryo axes 18:1 18:1 Total Seed No 14:0 16:0 16:1 18:0 n-9 n-7 18:2 18:3 DHS MVA STC CPFA B.1  0.6 25.1 0.5 3.4 12.0 0.6 44.5 0.7  2.2  7.0 3.0 12.2 B.2  0.6 26.3 0.5 3.5 11.2 0.6 44.3 0.6  2.4  6.5 2.7 11.6 B.3  0.7 26.1 0.4 4.0 10.6 0.6 41.6 0.7  3.1  8.1 3.2 14.4 B.4  0.7 26.7 0.4 3.9 11.5 0.6 42.0 0.6  2.8  7.1 3.0 12.9 B.5  0.6 27.2 0.5 3.7 12.0 0.6 45.0 0.4  2.2  4.4 2.7  9.3 B.6  0.6 27.3 0.5 3.6 11.4 0.6 42.4 0.6  2.7  6.7 2.9 12.3 B.7  0.7 27.2 0.5 3.5 11.6 0.6 43.9 0.6  2.4  5.7 2.7 10.8 B.8  0.6 26.6 0.4 4.1 11.5 0.6 42.8 0.5  2.7  6.4 2.9 12.0 B.9  0.7 26.2 0.4 3.8 11.3 0.6 44.6 0.5  2.4  6.0 2.7 11.2 B.10 0.7 26.8 0.5 3.8 11.6 0.6 42.4 0.6  2.7  6.6 3.0 12.3 B.11 0.7 26.4 0.5 3.3 10.8 0.7 42.8 0.8  2.4  7.9 3.1 13.4 B.12 0.7 27.0 0.4 3.9 11.5 0.6 43.1 0.6  2.4  6.3 2.7 11.4 B.13 0.7 26.5 0.5 3.9 12.0 0.6 42.9 0.6  2.6  6.3 2.8 11.6 B.14 0.7 26.5 0.5 3.7 11.7 0.6 43.7 0.6  2.5  6.1 2.7 11.3 B.15 0.6 26.9 0.5 3.5 12.2 0.6 44.1 0.5  2.3  5.5 2.6 10.3 B.16 0.6 26.4 0.5 3.3 12.2 0.6 48.0 0.4  1.8  4.2 1.9  8.0 B.17 0.6 26.6 0.5 3.7 11.5 0.6 43.4 0.6  2.6  6.4 2.7 11.8 B.18 0.6 28.8 0.5 4.1 11.2 0.7 39.2 0.7  2.3  7.9 3.2 13.5 B.19 0.7 26.0 0.5 3.2 11.2 0.7 45.3 0.7  2.0  6.5 2.7 11.1 B.20 0.6 26.8 0.5 3.8 10.7 0.6 43.0 0.7  2.1  7.6 3.0 12.7 B.21 0.7 27.2 0.5 3.6 11.3 0.6 40.7 0.7  3.0  7.3 3.6 13.9 B.22 0.7 26.4 0.5 3.2 11.8 0.7 44.5 0.6  2.0  6.2 2.6 10.9 B.23 0.5 24.6 0.5 2.9 12.7 0.6 51.4 0.4  1.0  3.3 1.5  5.8 Average  2.4  6.3 2.8 11.5

TABLE 4 Summary of sequence identifiers SEQUENCE ID NO: DESCRIPTION 1 cDNA sequence encoding cotton FAD2 from ghFAD2-1 gene. 1362 nucleotides, protein coding region: nucleotides 73-1227 2 amino acid sequence encoded by SEQ ID NO: 1: 384 amino acids 3 Nucleotide sequence of ghFatB-1 genomic DNA encoding acyl-acyl carrier protein thioesterase (FatB-1) from Gossypium hirsutum (Yoder et al., 1999 (supra)), Accession No. AF076535, 5201 bp. The complete cDNA sequence corresponds to nucleotides 915-1397, 1530-1663, 2352-2465, 2716-2887, 3001-3069, and 3322-3591 all joined together 4 amino acid sequence encoded by SEQ ID NO: 3: 413 amino acids 5 cDNA sequence from ghFatB-2 gene, 1647 nucleotides, The protein encoding region is from nucleotides 210 to 1472 (TAG stop codon) 6 amino acid sequence encoded by SEQ ID NO: 5: 420 amino acids 7 cDNA sequence from ghFatB-3 gene, 1498 nt 8 amino acid sequence encoded by SEQ ID NO: 7: 418 amino acids 9 EST sequence from G. hirsutum (Dowd et al., 2004 (supra)). Accession No. CD486555 10 Nucleotide sequence of ghCPA-FAS-1 encoding Gossypium hirsutum cyclopropane fatty acid synthase (CPA-FAS-1), Accession No. AY574036, complete cDNA sequence, 2884 bp, protein coding region: nucleotides 33-2654 11 amino acid sequence encoded by SEQ ID NO: 10: 873 amino acids 12 Nucleotide sequence of ghCPA-FAS-2 encoding Gossypium hirsutum cyclopropane fatty acid synthase (CPA-FAS-2), Accession No. AY574037, complete cDNA sequence, 2827 bp, protein coding region: nucleotides 16-2613 13 amino acid sequence encoded by SEQ ID NO: 12: 865 amino acids 14 Nucleotide sequence of ghCPA-FAS-3 encoding Gossypium hirsutum cyclopropane fatty acid synthase (CPA-FAS-3), Accession No. AY574038, complete cDNA sequence, 2912 bp, protein coding region: nucleotides 109-2706 15 amino acid sequence encoded by SEQ ID NO: 4: 865 amino acids 16 Fragment A of MonoCott, comprising the seed- specific lectin promoter derived from soybean lec1 gene: 1771 nucleotides 17 Fragment B of MonoCott, chimeric DNA of three target gene fragments 18 Fragment C of MonoCott: Intron from ghFAD2-1 19 Fragment D of MonoCott, complement of the chimeric DNA 20 Fragment E of MonoCott, lectin gene transcription terminator/polyadenylation region 21 Fragment F of MonoCott, S1 promoter 22 Fragment G of MonoCott, NPTII gene 23 Fragment H of MonoCott, S3 gene transcription terminator/polyadenylation region 24 Gossypium hirsutum mRNA for omega-6 desaturase (FAD2-1) also known as oleoyl-delta12 desaturase. Accession No. X97016 1386 bp protein coding region: nucleotides 54-1211. Homology with SEQ ID NO: 1 was 96% along the full length of the cDNAs 25 amino acid sequence encoded by SEQ ID NO: 24: 385 amino acids 26 cDNA sequence from ghFAD2-2 gene, Accession No. Y10112 (Liu et al., 1999), 1422 nucleotides, protein coding region: nucleotides 98-1249 27 amino acid sequence encoded by SEQ ID NO: 26: 383 amino acids 28 Complete cDNA sequence of Gossypium arboreum P450 monooxygenase gene, Accession No. AF332974, 1933 nt, protein coding region nucleotides 91-1701 29 sense primer for amplification of nucleotides 210 to 713 of SEQ ID NO: 3 30 antisense primer for amplification of nucleotides 210 to 713 of SEQ ID NO: 3 31 sense primer for amplification of nucleotides 1420 to 1821 of SEQ ID NO: 28 32 antisense primer for amplification of nucleotides 1420 to 1821 of SEQ ID NO: 28

TABLE 5 Exemplary and Preferred Amino Acid Substitutions Original EXEMPLARY PREFERRED Residue SUBSTITUTIONS SUBSTITUTIONS Ala Val, Leu, Ile Val Arg Lys, Gln, Asn Lys Asn Gln, His, Lys, Arg Gln Asp Glu Glu Cys Ser Ser Gln Asn, His, Lys, Asn Glu Asp, Lys Asp Gly Pro Pro His Asn, Gln, Lys, Arg Arg Ile Leu, Val, Met, Ala, Phe, Norleu Leu Leu Norleu, Ile, Val, Met, Ala, Phe Ile Lys Arg, Gln, Asn Arg Met Leu, Ile, Phe Leu Phe Leu, Val, Ile, Ala Leu Pro Gly Gly Ser Thr Thr Thr Ser Ser Trp Tyr Tyr Tyr Trp, Phe, Thr, Ser Phe Val Ile, Leu, Met, Phe, Ala, Norleu Leu

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1-45. (canceled)
 46. A cotton plant of the species Gossypium hirsutum which produces cottonseed which comprises oil, wherein in the oil of the cottonseed 72% to 88% by weight of the total fatty acid content is oleic acid, 4% to 16% by weight of the total fatty acid content is palmitic acid and 4% to 15% by weight of the total fatty acid content is linoleic acid, and wherein the cottonseed has a reduced level of each of cotton FAD2-1 protein, cotton FatB-2 protein and cotton CPA-FAS-2 protein relative to the levels of cotton FAD2-1 protein, cotton FatB-2 protein and cotton CPA-FAS-2 protein, respectively, in cottonseed of cotton variety Coker when grown under the same conditions.
 47. The cotton plant of claim 46, wherein 0.1% to 0.5% by weight of the total fatty acid content in the cottonseed oil is cyclopropane fatty acid (CPA), cyclopropene fatty acid (CPE) or a combination of CPA and CPE.
 48. The cotton plant of claim 47, wherein the fatty acid of the CPA or the CPE is malvalic acid, sterculic acid, dihydrosterculic acid or any combination of two or all three of these fatty acids.
 49. The cotton plant of claim 46, wherein the level of gossypol in the cottonseed is reduced by at least 10% relative to the level of gossypol in cottonseed of cotton variety Coker.
 50. The cotton plant of claim 46, wherein 4% to 10% by weight of the total fatty acid content in the cottonseed oil is palmitic acid.
 51. The cotton plant of claim 46, wherein the cottonseed has a germination rate which is substantially the same as cottonseed of the cotton variety Coker.
 52. The cotton plant of claim 46, wherein i) 0.1% to 0.5% by weight of the total fatty acid content in the cottonseed oil is cyclopropane fatty acid (CPA), cyclopropene fatty acid (CPE) or a combination of CPA and CPE, and ii) the level of gossypol in the cottonseed is reduced by at least 10% relative to the level of gossypol in cottonseed of cotton variety Coker.
 53. A process for producing cottonseed, comprising harvesting lint from the cotton plant of claim 46 and ginning the lint, thereby producing the cottonseed.
 54. The process of claim 53, wherein 0.1% to 0.5% by weight of the total fatty acid content in cottonseed oil of the cottonseed is cyclopropane fatty acid (CPA), cyclopropene fatty acid (CPE) or a combination of CPA and CPE.
 55. The process of claim 54, wherein the fatty acid of the CPA or the CPE is malvalic acid, sterculic acid, dihydrosterculic acid or any combination of two or all three of these fatty acids.
 56. The process of claim 53, wherein the level of gossypol in the cottonseed is reduced by at least 10% relative to the level of gossypol in cottonseed of cotton variety Coker.
 57. The process of claim 53, wherein 4% to 10% by weight of the total fatty acid content in cottonseed oil of the cottonseed is palmitic acid.
 58. The process of claim 53, wherein the cottonseed has a germination rate which is substantially the same as cottonseed of the cotton variety Coker.
 59. The process of claim 53, wherein i) 0.1% to 0.5% by weight of the total fatty acid content in cottonseed oil of the cottonseed is cyclopropane fatty acid (CPA), cyclopropene fatty acid (CPE) or a combination of CPA and CPE, and ii) the level of gossypol in the cottonseed is reduced by at least 10% relative to the level of gossypol in cottonseed of cotton variety Coker. 